20180606 AndrejSali CurriculumVitae...2018/06/06 · 2016 Speaker at the EMBL Distinguished Lecture Series, Heidelberg, Germany, January 12, 2016. 2016 Organizer and Speaker at the

Prepared: June 6, 2018

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University of California, San Francisco

CURRICULUM VITAE

Name: Andrej Sali, PhD Position: Professor, Step A/S Bioengineering & Therapeutic Sciences School of Pharmacy Address: Box 2552

1700 4th Street, 503B University of California, San Francisco San Francisco, CA 94158

Voice: 514-4227 Fax: 514-4231 Email: [email protected]

EDUCATION 1983 - 1987 University of Ljubljana, Slovenia BSC Chemistry

1987 - 1991 University of London, UK PhD Molecular Biophysics

PRINCIPAL POSITIONS HELD 1987 - 1991 Birkbeck College, and Imperial Cancer

Research Fund, London, UK. (Mentor: Prof. Thomas L. Blundell, FRS).

PhD student Crystallography

1991 - 1994 Harvard University, Cambridge, USA. (Mentor: Prof. Martin Karplus).

Postdoctoral Fellow

Chemistry

1995 - 2000 The Rockefeller University Assistant Professor

2000 - 2003 The Rockefeller University Associate Professor

2003 - present University of California, San Francisco Professor BTS

OTHER POSITIONS HELD CONCURRENTLY 2009 - 2012 California Institute for Quantitative

Biosciences (QB3) at UCSF Director

2003 - 2015 UCSF Vice Chair Department of Bioengineering and Therapeutic Sciences


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2003 - present California Institute for Quantitative Biosciences (QB3)

Faculty Member

2003 - present UCSF Faculty Member Pharmaceutical Sciences and Pharmacogenomics Graduate Program

2003 - present UCSF Faculty Member Biophysics Graduate Program

2003 - present UCSF Faculty Member Bioinformatics and Medical Informatics Graduate Program

2003 - present UCSF Faculty Member Chemistry and Chemical Biology Graduate Program

2015 - present School of Pharmacy, UCSF Associate Dean for Research

HONORS AND AWARDS 1984 Undergraduate scholarship J. Stefan Institute, Ljubljana, Slovenia.

1985 British Council Visiting Student Birkbeck College, London, UK.

1987 British Council Visiting Student Birkbeck College, London, UK.

1987 Overseas Research Students Award (1987-1990)

Committee of Principals and Vice Chancellors, England.

1987 Scholarship for graduate studies (1987-1988)

Research Council of Slovenia.

1989 Academic Scholarship (1989-1990) Merck Sharp & Dohm

1991 Postdoctoral Fellow (1991-1994) Jane Coffin Childs Memorial Fund for Medical Research

1996 Alexandrine and Alexander L. Sinsheimer Scholar (1996-1999)

Alexandrine and Alexander L. Sinsheimer Foundation

1998 Alfred P. Sloan Research Fellow (1998-2000)

Alfred P. Sloan Foundation

2000 Irma T. Hirschl Career Award Scientist (2000-2003)

Irma T. Hirschl Foundation

2007 Zois Award, Science Ambassador Republic of Slovenia

2014 Fellow International Society for Computational Biology (ISCB)

2015 Apple Teaching Award School of Pharmacy, UCSF


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2017 Academy Jubilee Professorship Indian Academy of Sciences

2018 Bijvoet Medal Utrecht University, Netherlands

2018 Member National Academy of Sciences, USA

KEYWORDS/AREAS OF INTEREST Structural biology, computational biology, bioinformatics, proteins, macromolecular complexes, assemblies, macromolecular processes, sequence, structure, function, evolution, modeling of protein structure, prediction of protein function. We employ the laws of physics and the rules of evolution to develop and apply methods for:

• predicting the structures of proteins; • determining the structures of macromolecular assemblies; • annotating the functions of proteins and their assemblies using their structures.

PROFESSIONAL ACTIVITIES

MEMBERSHIPS 1991 - present Protein Society

1991 - present American Association for the Advancement of Science

2007 - present Biophysical Society

2014 - present International Society for Computational Biology

SERVICE TO PROFESSIONAL ORGANIZATIONS 2005 - 2008 Protein Society Executive

Committee

2005 - present Protein Data Bank Scientific Advisory Committee

2009 - 2013 PROSPECTS (Proteomics Specification in Time and Space) consortium

Scientific Advisory Committee

2010 - 2010 Keystone Symposia Scientific Advisory Board (ad hoc)

2011 - 2015 Keystone Symposia Scientific Advisory Board

2010 - present Protein Data Bank Electron Microscopy Validation Task Force (Co-Chair)

2010 - present Protein Data Bank Small Angle Scattering Task Force


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2014 - present Protein Data Bank Hybrid Models Task Force (Co-Chair)

2010 - present Electron Microscopy Data Bank Scientific Advisory Committee

2009 - present PSI Knowledgebase Working Group on Theoretical Structural Model Validation

2011 - present Rosetta Commons Scientific Advisory Board

2017 - 2019 Biophysical Society Committee member of BPS

SERVICE TO PROFESSIONAL PUBLICATIONS 2003 - present Editor, Structure.

2004 - present Editorial Board, PLoS Computational Biology.

2002 - present Editorial Board, Journal of Computer Aided Molecular Design.

2002 - present Editorial Board, Molecular and Cellular Proteomics.

2004 - present Editorial Board, Protein Engineering, Design, and Selection.

2001 - present Section Head for the Structural Genomics section on BioMed Central

1990 - present Reviewer for Nature, Science Cell, Proc. Natl. Acad. Sci. USA, Nature Structural and Molecular Biology Nature Genetics, Nature Biotechnology, Structure, Journal of Molecular Biology, Proteins, Protein Engineering, Design, and Selection, Protein Science, Bioinformatics, Nucleic Acids Research, Journal of Biological Chemistry, BMC Structural Biology, Genome Biology, FEBS Letters, Journal of Computer Aided Molecular Design, Biophysical Journal, Biochemical Journal, PLoS Biology, and PLoS Computational Biology.

INVITED PRESENTATIONS - INTERNATIONAL 1999 CERCA CADD Symposium, Montreal, Canada. April 13,

1999.

1999 Data Mining in Crystallography, Erice, Italy. May 15, 1999.

1999 Structural Biology Net, Tallberg, Sweden. June, 1999.

1999 Frontiers in Structural Biology, Indian Institute of Science, Bangalore, India. August 27, 1999.

1999 BRI, Montreal, Canada. November 24, 1999.

1999 University of Toronto, Toronto, Canada. December 9, 1999.


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2000 Japan Biophysical Society Meeting, Tokyo, Japan. January 17, 2000.

2000 Bioinformatics 2000, Elsinore, Denmark. April 28, 2000.

2001 University of Zuerich, Zuerich, Switzerland. December 5, 2001.

2001 Bioinformatics & Proteomics: From Sequence to Function, Lausanne, Switzerland. December 6, 2001.

2001 Structural Genomics and Bioinformatics, Instituto Juan March, Madrid, Spain. March 12-14, 2001.

2001 Annual meeting of the Canadian Society for Biochemistry and Molecular and Cellular Biology (CSBMCB), Toronto, Canada. May 31-June 3, 2001.

2001 Math/Chem/Comp 2001, Dubrovnik, Croatia. June 25-30, 2001.

2001 4th International Conference on Biological Physics, ICBP2001, Kyoto, Japan. July 30-August 3, 2001.

2001 4th International Conference on Molecular Structural Biology, ICMSB2001, Vienna, Austria. September 5-9, 2001.

2001 Genomics & Proteomics meeting, Barcelona, Spain. October 19, 2001.

2002 University of Barcelona, Barcelona, Spain. May 21, 2002.

2002 Genomics & Proteomics meeting, Barcelona, Spain. May 22, 2002.

2002 Samuel Lunenfeld Research Institute, Toronto, Canada. May 29, 2002.

2002 The 19th Congress and General Assembly of the International Union of Crystallography IUCR, Geneva, Switzerland. August 6-15, 2002.

2002 Genomics and Bioinformatics Center Inaugural Symposium, Pontificia Universidad Catolica, Santiago, Chile. November 18-20, 2002.

2003 Fourteenth Annual World Molecular Engineering Network (WMEN) Conference, San Jose del Cabo, Baja California Sur, Mexico. May 4-8, 2003.

2003 5th Meeting of the Slovenian Biochemical Society, Ljubljana, Slovenia. September 24-28, 2003.

2004 University of Cologne, Cologne, Germany. January 19, 2004.


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2004 Ringberg meeting, Schloss Ringberg, Germany. January 21-23, 2004.

2004 Fourteenth Annual World Molecular Engineering Network (WMEN) Conference (2004), San Jose del Cabo, Baja California Sur, Mexico. May 2-6, 2004.

2004 EMBO conference on Structures in Biology, EMBL, Heidelberg, Germany. November 10-13, 2004.

2005 The 7th World Congress of the World Association of Theoretically Oriented Chemists (WATOC), Capetown, South Africa. January 16-21, 2005.

2005 Keynote Speaker in XX IUCr Congress in Firenze, Italy. August 23-31, 2005.

2005 Speaker at the International Workshop M2CELL, The Royal Abbey of Fontevraud, Paris, France. December 4-6, 2005.

2006 Organizer and Speaker at the World Molecular Engineering Network Conference. Cabo San Lucas, Mexico. April 30-May 2nd, 2006.

2006 Plenary Speaker at the 11th Symposium on Recent Advances in Biophysics, National Taiwan University, Taipei, Taiwan. May 23-26, 2006

2006 2006 Keystone Symposium on Multi-Protein Complexes Involved in Cell Regulation, St. John's College, Cambridge, UK. August 18-23, 2006.

2007 Organizer and Speaker at the World Molecular Engineering Network Conference. Cabo San Lucas, Mexico. April 29-May 2nd, 2007.

2007 Protein Complexes and Protein Networks Symposium in Martinsried, Germany, May 21-22, 2007.

2007 Symposium on Structural Biology and its Application to Drug Development at the University of Tokyo, Tokyo, Japan, 28 January 2007.

2008 Invited Speaker at the Basel Computational Biology Conference [BC]2 , Basel, Switzerland, March 13-14, 2008.

2008 Organizer and Speaker of the World Molecular Engineering Network Conferenc. Cabo San Lucas, Mexico. May 4-8, 2008.

2008 University of Toronto, Canada, 26 July, 2008.

2008 Speaker at the 40th Course: From Molecules to Medicines Integrating Crystallography in Drug Discovery, Erice, Italy. May 29 - June 8, 2008.


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2008 Speaker at the Gordon Research Conference on Macromolecular Organization & Cell Function: Systems Cell Biology, Oxford, England, July 27 to August 2, 2008.

2008 Speaker at the 6th National NCCR Symposium on New Trends in Structural Biology, Zurich, Switzerland, September 8-9 2008.

2008 Speaker at the Max Planck Institute, Student Workshop, Goettingen, Germany. September 10-13 2008.

2008 Speaker at the Max Planck Institute of Biochemistry, INSTRUCT Open Meeting, in Martinsried, Germany, October 16-17 2008.

2009 Speaker at the NoE 3DEM final Meeting, Brdo, Slovenia, February 9-13, 2009.

2009 McDowell Lecture at the University of British Columbia, Vancouver, BC, Canada, March 10, 2009.

2009 Seminar at the University of Ljubljana, Ljubljana, Slovenia, December 17, 2009.

2010 Organizer and Speaker at the 20th World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 2-5, 2010.

2010 Speaker at the Institute of Structural Molecular Biology, Birkbeck Institute, London, England, June 17-18, 2010

2010 Speaker at the MPIMP Dahlem Colloquia in Molecular Genetics, Max Planck Institute, Berlin, Germany, August 22-24, 2010.

2010 Speaker at Exeter College, Oxford University, England, October 4, 2010.

2010 Speaker at the PROteomics SPECification in Time and Space - PROSPECTS Meeting, Taormina, Sicily, Italy, November 2-4, 2010.

2010 Speaker at the 6th International Conference on Structural Biology and Functional Genomics, National University of Singapore, Singapore, December 6-8, 2010.

2011 Organizer and Speaker at the 21st World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 1-4, 2011.

2011 Speaker at the International Conference on Structural Genomics, University of Toronto, Toronto, Ontario, Canada, May 10-14, 2011.

2011 Speaker at IGBMC, Strasbourg, France, July 17-18, 2011.


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2011 Speaker at Max Planck Institute, Munich, Germany, July 20-21, 2011.

2011 Plenary Speaker at the ComBio 2011, Cairns Convention Centre, Cairns, Australia, September 26-29, 2011.

2012 Plenary Speaker at the Molecular Modeling Meeting, Queenstown, New Zealand, August 30-September 1, 2012.

2013 Speaker at the Swiss Federal Institute of Technology, Lausanne, Switzerland, January 14, 2013.

2013 Speaker at the Biozentrum Lecture, Basel, Switzerland, January 15, 2013.

2013 Organizer and Speaker at the 23rd World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 5-8, 2013.

2013 Speaker at the Bioinformatics Meeting, Recife, Brazil, November 3-7, 2013.

2014 Speaker at the Lorne Conference, Victoria, Australia, February 9-13, 2014.

2014 Speaker at Shanghai Tech University, Shanghai, China, March 14-18, 2014

2014 Organizer and Speaker at the 24th World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 4-7, 2014

2014 Keynote Speaker at the Emerging Trends in Computational Biology Conference, Singapore, June 20-21, 2014

2014 Speaker at the PDB Hybrid Methods Task Force Meeting, EMBL-EBI, HInxton, UK, October 6-7, 2014

2015 Seminar at A*Star BII, Singapore, March 12-14, 2015

2015 Organizer and Speaker at the 25th World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 3-6, 2015

2015 Speaker at the GRC on Computational Aspects of Biomolecular NMR, Il Ciocco, Italy, June 7-12, 2015

2015 Speaker at the 29th Annual Symposium of the Protein Society, Barcelona, Spain, July 22-25, 2015

2015 Seminar at Pasteur Institute, Paris, June 24, 2015

2015 Speaker at iHuman Institute, Shanghai Tech University, Shanghai, China, July 27-31, 2015


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2015 Keynote Speaker at the FEBS3+ Meeting "Molecules of Life", Portoroz, Slovenia, September 16-19, 2015.

2015 Speaker at the Hybrid Methods Meeting, Osaka, Japan, October 2-4, 2015

2015 Speaker at the Advances in Integrative Biology of Cellular Processes, Shanghai, China, November 10-12, 2015.

2016 Speaker at the Graduate School of Quantitative Biosciences Munich (QBM), Munich, Germany, January 11, 2016.

2016 Speaker at the EMBL Distinguished Lecture Series, Heidelberg, Germany, January 12, 2016.


2016 Speaker at the ETH Zurich Department of Biology Symposium, Zurich, Switzerland, June 13-15, 2016.

2016 Speaker at the Max F. Perutz Laboratories, The IMP, Vienna, Austria, June 28-29, 2016.

2017 Speaker at the Bioimaging Data Repositories Workshop, EMBL-EBI, Hinxton, UK, Jan 23-24, 2017.

2017 Speaker at the Frontiers of NMR in Life Sciences, Keystone, CO, March 12-17, 2017.


2017 Seminar at the Sophia College for Women, Mumbai, Jul 24, 2017.

2017 Seminar at the Tata Institute for Fundamental Research, Mumbai, Jul 24, 2017.

2017 Seminar at the Dept. of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Jul 26, 2017.

2017 Seminar at the Ahmednagar College, Ahmednagar, Jul 28, 2017.

2017 Seminar at the Indian Institute of Science Education and Research, Pune, Jul 31, 2017.

2017 Seminar at the Institute of Bioinformatics and Biotechnology, Pune University, Pune, Aug 1, 2017.

2017 Seminar at the National Center for Biological Sciences, Bangalore, Aug 2, 2017.


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2017 Seminar at the Indian Institute of Sciences, Bangalore, Aug 3, 2017.

2017 Seminar at the Mysore College, Mysore, Aug 4, 2017.

2017 Seminar at the Molecular Biophysics Unit, Indian Institute of Sciences, Bangalore, Aug 7, 2017.

2017 Speaker at the Conformational ensembles from experimental data and computer simulations, Biophysical Society, Berlin, Germany, Aug 25-29, 2017.

2017 Speaker at the QBI 2017 Cell Mapping Symposium, UCSF, San Francisco, CA, Sep 13-14, 2017.

2017 Speaker at the iHuman Institute at ShanghaiTech Symposium, Shanghai, China, Nov 7-8, 2017.

2017 Speaker at the EMBL/EMBO Symposium: From Single- to Multiomics: Applications and Challenges Data Integration, Heidelberg, Germany, November 12-14, 2017.

2017 Speaker at the Revolutions in Structural Biology: Celebrating the 100th anniversary of Sir John Kendrew, EMBL, Heidelberg, Germany, Nov 16-17, 2017.

2018 Speaker at the 3rd DNA Replication and Repair Structures & Cancer Conference, Cancun, Mexico, Feb 11-15, 2018.

2018 Keynote Speaker at the 2018 Annual Symposium of the Bijvoet Center of Biomolecular Research, Utrecht, Netherlands, Apr 23-24, 2018.


INVITED PRESENTATIONS - NATIONAL 1999 Second International Georgia Tech Conference in

Bioinformatics, Atlanta, Georgia, USA. November 12, 1999.

1999 2.Structural Genomics Targets Workshop, NIH, Washington DC, USA. February 11, 1999.

1999 Advances & Opportunities at the Biology/Math/Computational/Physical Sciences Interface, Rutgers University, New Brunswick, NJ, USA. March 6, 1999.

1999 Mount Sinai School of Medicine, New York, NY, USA. March 19, 1999.

1999 New York Structural Biology Group, New York Academy of Sciences, New York, NY, USA. March 24, 1999.


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1999 Columbia University, New York, NY, USA, 1999.

1999 Chemistry Dept., New York University, New York, NY, USA, 1999.

1999 Protein Sequence Structure Function Meeting, UCSF, San Francisco, CA, USA. April 23, 1999.

1999 The Scripps Institute, La Jolla, CA, USA. August 13, 1999.

1999 Mathematical Problems in the Molecular Sciences, Courant Institute, New York, NY, USA. October 10, 1999.

1999 City College of New York, New York, USA. October 20, 1999.

1999 Agouron Pharmaceuticals, San Diego, California, USA. October 28, 1999.

1999 Structural Genomics Conference, ANL, Chicago, Illinois, USA. November 16, 1999.

1999 Structural Genomics and the Pharmaceutical Industry, Princeton, New Jersey, USA. November 18, 1999.

2000 Quantitative Challenges in the Post Genomic Sequence Era, La Jolla Interfaces in Science, San Diego, California, USA. January 12, 2000.

2000 UCSD, Dept of Physics, San Diego, California, USA. January 19, 2000

2000 UCSF, San Francisco, California, USA. January 20, 2000.

2000 Center for Physics and Biology, Rockefeller University,New York, New York, USA. January 24, 2000.

2000 Biological Chemistry Seminar Series, University of Penn, Philadelphia, Pennsylvania, USA. February 17, 2000.

2000 ABRF 2000 ``From Singular to Global Analyses of Biological Systems'', Bellevue, Washington, USA. February 22, 2000.

2000 AAAS conference, Washington DC, USA. March 20, 2000.

2000 Keystone Symposium on Macromolecular Assemblies at Work: Application of Physics, Chemistry, and Mathematics to Biology, Durango, Colorado, USA. March 25, 2000.

2000 Bio2000, Boston, Massachusetts, USA. March 28, 2000

2000 Computational Challenges of the Post Genomic Age, SUN, San Francisco, California, USA. May 12, 2000.

2000 Biopolymers Gordon Conference, Newport, Rhode Island, USA. June 18-22, 2000.


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2000 2000 FASEB Summer Research Conference on Protein Folding in the Cell, Saxton River, Vermont, USA. July 22-27, 2000.

2000 Monsanto/Pharmacia lectureship series, Univ. of Saint Louis, Missouri, USA. September 28, 2000.

2000 Workshop on Structural Genomics. NIGMS, Washington DC, USA. October 23, 2000.

2000 Genomics and Bioinformatics, UMD, New Brunswick, New Jersey, USA. November 2, 2000.

2000 University of Minnesota, Minneapolis, Minnesota, USA. November 27, 2000.

2001 Oncogenomics: Dissecting Cancer Through Genome Research, Nature Genetics, Tuscon, Arizona, USA. January 25-27, 2001.

2001 UAB, Birmingham, Alabama, USA. February 26, 2001.

2001 Bard College, New York, USA. April 18, 2001.

2001 Physics/Chemistry. CSUN, Northridge, California, USA. May 2, 2001.

2001 ACS Meeting, Chicago, Illinois, USA. August 26-30, 2001.

2001 University of Maryland, Maryland, USA. October 2, 2001.

2001 Columbia University, New York, New York, USA. October 15, 2001.

2001 Mast Cell Workshop, Bethesda, Maryland, USA. November 26-30, 2001.

2002 Genomics Seminar Series, Skirball Institute, New York, New York, USA. February 6, 2002.

2002 Mining the Human Genome for New Drug Discovery - New Ways of Handling Orphan Targets. NYAS, New York, New York, USA. February 26, 2002.

2002 Biological Processes for New and Innovative Engineering Systems and Applications, ARO workshop, Research Triangle Park, North Carolina, USA. February 26-27, 2002.

2002 New York City Blood Centre, New York, New York, USA. March 7, 2002.

2002 Proteomics - The New Frontiers: Discovery, Separation, Prediction & Modeling, University of Delaware, Newark, Delaware, USA. March 14-15, 2002.


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2002 Harvard University, Cambridge, Massachusetts, USA, March 28, 2002.

2002 Molecular Cell Biology and Biochemistry Seminar Series, Virginia Tech, Blacksburg, Virginia, USA. April 5, 2002.

2002 UCSF, San Francisco, California, USA, April 15, 2002.

2002 A Workshop on large biological structures, Asilomar, California, USA. April 20-22, 2002.

2002 SCBMB Program, Baylor College of Medicine, Houston, Texas, USA. May 15, 2002.

2002 50th ASMS conference American Society of Mass Spectrometry, Orlando, Florida, USA. June 2-6, 2002.

2002 The 5th Summer Session of the New York Structural Biology Discussion Group , Cold Spring Harbor Laboratory, New York, USA. June 26, 2002

2002 Berkeley-Stanford summer school for protein crystallography, SSRL, Stanford, California, USA. July 8-12, 2002.

2002 Gordon Conference on Diffraction Methods in Structural Biology, Connecticut College, New London, Connecticut, USA. July 14-19, 2002.

2002 NYCBS New York Computational Biology Society seminar, NAS, New York, New York, USA. September 18, 2002.

2002 Center for Biological Modeling, Michigan State University, East Lansing, Michigan, USA. September 27, 2002.

2002 Bioinformatics seminar, Texas A&M University, Tamu, TX, USA. November 7, 2002.

2002 Structure and Function of the Proteome, Argonne National Laboratory, Argonne, Illinois, USA. November 23-24, 2002.

2003 Keystone Symposium in Proteomics: Technologies and Applications, Keystone Resort in Keystone, Colorado, USA. March 25-30, 2003.

2003 NCRR sponsored Workshop on Structural Proteomics of Complexes, Bethesda, Maryland, USA. April 7-8, 2003.

2003 American Society for Biochemistry and Molecular Biology meeting, San Diego, California, USA. April 11-15, 2003.

2003 St. Jude Children's Research Hospital, Memphis, TN, USA. April 22, 2003.

2003 Genentech, Inc., South San Francisco, CA, USA. April 29, 2003.


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2003 Structure and Function of Proteome, SBC, Argonne National Laboratory, Argonne, Illinois, USA. Spring, 2003.

2003 "Frontiers of Bioinformatics" symposium, Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York, USA. June 6-8, 2003.

2003 IBM Thomas J. Watson Research Center, New York, New York, USA. June 11, 2003.

2003 2003 Gordon Research Conference on 3D Electron Microscopy of Macromolecules, Colby Sawyer College, New London, New Hampshire, USA. June 22-26, 2003.

2003 PSI workshop ond data management, NIH Campus, Bethesda, MD, USA. July 10-11, 2003.

2003 GTL and Beyond: Data and Computational Needs Workshop, San Francisco, CA, USA. September 10-11, 2003.

2003 2003 Pharmaceutical Sciences and Pharmacogenomics Retreat, Marshall, CA, USA. September 11-13, 2003.

2003 Structure and Chemistry Seminar at Scripps, San Diego, CA, USA. September 18, 2003.

2003 Seminar at Northeastern University, Boston, MA, USA. October 6, 2003

2003 Workshop on Visualization of Biological Complexes, Four Points Sheraton Hotel, Emeryville, San Francisco Bay Bridge, CA, USA. October 11-12, 2003

2003 Seminar at PARC, Palo Alto, CA, USA. October 15, 2003.

2003 NIGMS Homology Modeling Workshop, Bethesda, MD, USA. October 21-22, 2003.

2003 Seminar at Purdue University, West Lafayette, IN, USA. October 24-25, 2003.

2003 PSI Target Selection Workshop, Bethesda, MD, USA. November 13-14, 2003.

2003 Biophysics/CCB Retreat, Asilomar Conference Center, Pacific Grove, CA, USA. December 7-9, 2003.

2004 Licensing Executives Society meeting, San Francisco, CA, USA. February 12, 2004

2004 The Structural, Functional and Evolutionary Gordon Conference, Four Points Sheraton Harbortown, Ventura, CA, USA. February 15-20, 2004.

2004 Seminar at Berkeley, Berkeley, CA, USA. March 8, 2004.


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2004 Seminar at UCSC, Santa Cruz, CA, USA. March 11, 2004.

2004 Workshop on Structure Determination of Macromolecular Machines and Assemblies by Hybrid Methods, Granlibakken/Lake Tahoe Conference Center, CA, USA. March 17-20, 2004.

2004 Workshop on Structural Determination of Environmentally Responsive Gene (ERG) Products for Diagnostics & Drug Discovery (NIEHS/DERT), Snowbird Resort, Snowbird, Utah, USA April 12-13, 2004.

2004 2004 Keystone Symposium on Structural Genomics, Snowbird Resort, Snowbird, Utah, USA April 13-19, 2004.

2004 BayGenomics PGA, San Francisco, CA, USA. April 27, 2004.

2004 Gladstone Scientific Retreat, Asilomar in Monterey County, CA, USA. May 18-20. 2004.

2004 Seminar at Caltech, Pasadena, CA, USA. October 12, 2004.

2004 ICSG 2004 Meeting, Washington, DC, USA. November 17-24, 2004.

2004 Workshop of the Center of Protein Folding Machinery, Stanford University, CA, USA. December 4-5, 2004.

2004 Biological and Medical Informatics/Biophysics/Chemistry and Chemical Biology graduate groups retreat, Asilomar Conference Center, Pacific Grove, CA, USA. December 5-7, 2004.

2005 ABRF meeting, Biomolecular Technologies:Discovery to Hypothesis, Savanah, Georgia, USA. February 5-8, 2005.

2005 Frontiers in Computational Biophysics Symposium, NIH campus in Bethesda, MD, USA. April 29-30, 2005.

2005 NIH Symposium on Structural Analysis of Large Assemblies: Sizing up the Challenges, NIH campus in Bethesda, MD, USA. June 2-3, 2005.

2005 SRI’s Computational Biology series, SRI International, Menlo Park, CA, USA. June 29, 2005.

2005 19th Annual Symposium of the Protein Society, Boston, MA, USA. July 30 – August 3, 2005.

2005 GRC 2005 Computer-aided design meeting, Tilton School, NH, USA. July 31 – August 5, 2005.

2005 Seminar at the Biochemical and Biophysical Methods Course Fall 2005, The Rockefeller University, New York, NY, USA. October 11, 2005.


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2005 Seminar at the Novartis Institutes for BioMedical Research, Cambridge, MA, USA. November 9, 2005.

2005 Workshop on Biological Macromolecular Structure Models, The State University of New Jersey, Piscataway, NJ, USA. November 19-20, 2005.

2006 Organizer and Speaker of the Theme “Macromolecular Structure and Dynamics” with 4 Symposia. ASBMB 2006 meeting, San Francisco, CA, USA. April 1-5, 2006.

2006 Seminar at UC Davis, CA. June 1, 2006.

2006 Symposium at Wyeth Research, Cambridge, MA, USA. October 16, 2006.

2006 Seminar at the University of Massachusetts, Dept. of Biochemistry and Molecular Pharmacology, Worcester, MA, USA. October 18, 2006.

2006 Seminar at the Fifth Annual Systems Biology Course at the Institute for Systems Biology, Seattle, WA, USA. 9 November 2006.

2006 Seminar at UC Merced Center for Computational Biology, Merced, CA, USA. 30 November 2006.

2006 TDR/WHO Drug Target Selection Meeting in Seattle, OR, USA. 1 December, 2006.

2006 Biological and Medical Informatics/Biophysics/Chemistry and Chemical Biology Graduate Groups Retreat, Monterey, CA, USA. 3-5 December, 2006.

2007 Collaborative Drug Discovery meeting, UCSF, San Francisco, USA. 1 March 2007

2007 The Protein Folding Center Annual Retreat, Stanford, CA, USA. 27-29 May 2007.

2007 Seminar at the Center for Theoretical Biological Physics. UCSD,San Diego USA. 1 June, 2007.

2007 Institute for Systems Biology, Seattle, WA, 12 July 2007.

2007 Seminar at Genentech, San Francisco, CA, 25 September 2007.

2007 Seminar at the SCRIPPS Institute, La Jolla, CA, USA. September 27-28

2007 Speaker and Organizer of the Modeling of Protein Interactions Meeting, MPI-2007, Lawrence, KA, USA, September 30 – October 2, 2007.


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2007 Seminar at the Albert Einstein College of Medicine, New-York, NY. 16 October 2007.

2007 Seminar at University of California Berkeley, New-York, NY. 25 October 2007.

2007 Seminar at the Carolina Center for Genomic Sciences colloquium, UNC, Chapel Hill, NC, USA. 9 November 2007.

2007 Seminar at the Duke University Computational Biology Series, Durham, NC, USA. 12 November 2007.

2008 Keystone Symposium on Structural Genomics and Its Applications to Chemistry, Biology and Medicine, Steamboat Springs, Colorado, CO, USA, 6-11 January 2008.

2008 Seminar for the Biochemical and Biophysical Methods Course at the Rockefeller University, New York, NY. 30 January 2008

2008 Seminar at the University of Utah, February 25 2008.

2008 Seminar at The Buck Institute for Age Research, Novato, CA, USA, July 1 2008.

2008 Speaker and Organizer of the Protein Modeling Workshop, University of California, San Francisco, CA, USA, July 11-12 2008.

2008 Speaker at the 2008 Senior Vice Chancellor’s Laureate Lecture Series at the University of Pittsburgh, July 18 2008.

2008 Protein Structure Initiative (PSI3), Washington DC, USA, October 29-30, 2008.

2008 Seminar at UT Southwestern Medical Center, 5-6 Nov 2008.

2008 Biology and Mathematics in the Bay Area (BaMBA), University of California, Davis, CA,USA, November 15, 2008.

2008 Biological and Medical Informatics/Biophysics/Chemistry and Chemical Biology Graduate Groups Retreat, Monterey, CA, USA. 7-9 December, 2008.

2008 NCMI Single Particle Reconstruction Workshop, Baylor College of Medicine, Houston, TX, USA, December 10-13, 2008.

2009 Seminar at the University of Pennsylvania School of Medicine, Philadelphia, PA, USA, January 29, 2009.

2009 Mesilla Chemistry Workshop Multi-Scale Modeling of Biological Molecules, Mesilla, TX, USA, February 1-4, 2009.

2009 Technology Centers for Networks and Pathways Annual All Hands Meeting, Washington DC, USA, March 12-13, 2009


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2009 2009 Symposium on Molecular Systems Biology of the Cell, Seattle, WA, USA, April 19, 2009.

2009 Seminar at the University of Minnesota, Minneapolis, MN, USA, April 22, 2009.

2009 Seminar at the University of Washington, Seattle, WA, USA, May 14, 2009.

2009 Seminar at Indiana University, Indianapolis, IN, USA, May 18, 2009.

2009 Seminar at University of Texas Southwestern, Dallas, TX, USA, May 20-21, 2009.

2009 23rd Annual Symposium of the Protein Society, Boston, MA, USA, July 25-29, 2009.

2009 Speaker at the Pharmaceutical Sciences and Pharmacogenomics Retreat, Tomales Bay, CA, USA, September 9-10, 2009.

2009 Beckman Institute 20th Anniversary Symposium, University of Illinois at Urbana-Champaign, Urbana, IL, USA, September 20-23, 2009.

2009 Seminar at University of Southern California, Los Angeles, CA, USA, November 19, 2009.

2009 Speaker at the Annual Computational and Theoretical Biology Symposium, Houston, TX, USA, December 4-6, 2009.

2010 Speaker and Co-Organizer of the Keystone Symposia on Structural Biology/Structural Genomics, Steamboat Springs, CO, USA, January 8-13, 2010.

2010 Speaker at the Modeling of Cryo-EM Map Workshop, Baylor College of Medicine, Houston, TX, USA, January 14-17, 2010.

2010 Chair and Speaker at the Biophysical Society 54th Annual Meeting, San Francisco, CA, USA, February 20-24, 2010.

2010 Speaker at the Hybrid Methods Symposium, Lake Tahoe, CA, USA, March 10-14, 2010.

2010 Speaker at the Structural Biology Symposium, Case Western Reserve University, Cleveland, OH, USA, May 19, 2010.

2010 Keynote Speaker at the 3Dsig Satellite Meeting, Boston, MA, USA, July 9-10, 2010.

2010 Speaker at the 18th International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, USA, July 11-13, 2010.


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2010 Seminar at Vanderbilt University, Nashville, TN, USA, October 12, 2010.

2010 Seminar at Ohio State University, Columbus, OH, USA, October 26, 2010.

2010 Speaker at the MPI Meeting, University of Kansas, Lawrence, KS, USA, October 28-30, 2010.

2010 Seminar at the University of California, San Diego, CA, USA, December 12, 2010.

2011 Speaker at the Design of Drugs and Chemicals that Influence Biology Workshop, University of California, Los Angeles, CA, USA, April 4-8, 2011.

2011 Keynote Speaker at the Sanford-Burnham Structural Systems Biology Symposium, La Jolla, CA, USA, June 7, 2011.

2011 Speaker at the Institute for Systems Biology Symposium and Workshop, University of Washington, Seattle, WA, USA, July 24-27, 2011.

2011 Speaker at the Accelerating Predictive Drug Development Through Quantitative Pharmacology Symposium University of California, San Francisco, California, USA, September 22-23, 2011.

2011 Speaker at the Worldwide Protein Data Bank (wwPDB) Symposium, Cold Spring Harbor, NY, USA, October 28-30, 2011.

2011 Seminar at St. Jude Children’s Research Hospital, Memphis, TN, USA, November 15, 2011.

2011 Seminar at Duke University, Durham, NC, USA, November 18, 2011.

2012 Speaker and Co-organizer of the Keystone Symposia on High Throughput and Hybrid Approaches to Structural Biology, Keystone, CO, USA, January 22-27, 2012.

2012 Speaker at Eli Lilly Symposium, Indianapolis, IN, USA, February 13-14, 2012.

2012 Seminar at the University of Michigan, Ann Arbor, MI, USA, February 15, 2012.

2012 Seminar at the Scripps Research Institute, San Diego, CA, USA, March 1-2, 2012.

2012 Co-organizer of the 6th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods, Lake Tahoe, CA, USA, March 14-18, 2012.


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2012 Keynote Speaker at the ISMB, Long Beach, CA, USA, July 14-17, 2012.

2012 Speaker at the NRAMM Workshop, Scripps Research Institute, San Diego, CA, USA, November 16, 2012.

2013 Seminar at NIH, Bethesda, MD, USA, January 17, 2013.

2013 Speaker at the Herron Lecture, Florida State University, Tallahassee, FL, USA, February 15, 2013.

2013 Speaker at the Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA, March 28, 2013.

2014 Seminar at Harvard University, Cambridge, MA, USA, February 3, 2014

2014 Seminar at Columbia University, New York, NY, USA, February 5, 2014

2014 Seminar at the Scripps Research Institute, San Diego, CA, USA, February 24-25, 2014

2014 Seminar at UC Berkeley, Berkeley, CA, USA, March 10, 2014

2014 Keynote Speaker at the 2014 Biopolymers Gordon Research Conference, Newport, RI, USA, June 1-6, 2014

2014 Keynote Speaker at the 2014 Annual RosettaCon, Leavenworth, WA, USA, July 30 - August 1, 2014

2014 Speaker at the Peter Wright Symposium, University of California, San Francisco, CA, USA, September 15, 2014

2014 Speaker at the NCI Workshop at the Houston Methodist Research Institute at Texas Medical Center, Houston, TX, USA, September 18-19, 2014

2014 Organizer of the Martin Karplus Celebration Symposium, San Francisco, CA, USA, October 1, 2014

2014 Speaker at the International Society for the Study of Xenobiotics meeting, San Francisco, CA, USA, October 19-23, 2014

2014 Seminar at Rutgers University, New Brunswick, NJ, USA, October 29, 2014

2015 Seminar and Biophysics Course at the Scripps Research Institute, San Diego, CA, USA, February 26-27, 2015

2015 Speaker at the U.S. Human Proteome Organization (US-HUPO) Annual Meeting, Tempe, AZ, USA, March 15-18, 2015

2015 Speaker at the American Chemical Society National Meeting, Denver, CO, USA, March 22-26, 2015


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2015 Seminar at the University of Florida, Gainesville, FL, USA, April 14, 2015

2015 Seminar at the Oregon Health and Science University, Portland, OR, USA, May 19, 2015

2015 Seminar at Department of Chemistry and Biochemistry, UCSD, San Diego, November 2-3, 2015.

2016 Speaker at the 2016 ASBMB Annual Meeting, San Diego, USA, April 6, 2016.

2016 Speaker at the 5th International Symposium on Higher Order Structure of Protein Therapeutics, Long Beach, USA, April 12, 2016.

2016 Organizer and Speaker at the Computational Biophysics Workshop, San Francisco Dec 12-16, 2016.

2017 Speaker at the QBI 2017 Cell Mapping Symposium, UCSF, San Francisco, CA, Sep 13-14, 2017.

2017 Seminar at the Rockefeller University, New York City, NY, Oct 24, 2017

2018 Speaker at the 2018 Keystone Symposia on Cryo-EM from Cells to Molecules: Multi-Scale Visualization of Biological Systems, Granlibakken, CA, Feb 4-9, 2018.

2019 Organizer of the 63rd Annual Meeting of the Biophysical Society, Baltimore, MD, Mar 2-6, 2019.

GOVERNMENT AND OTHER PROFESSIONAL SERVICE 2004 - 2009 National Institutes of Health MSF-B Study

Section (successor of BBCA)

1995 - present NIH, National Science Foundation ad hoc Grant Reviews

- DOE, European Community

- Burroughs Welcome Fund

- Binational Science Foundation

UNIVERSITY AND PUBLIC SERVICE

SERVICE ACTIVITIES SUMMARY I serve on a large number of committees at UCSF, as detailed on the cv; these include graduate program leadership, technical infrastructure, and faculty search committees. In addition, I am engaged in public service, for example as an editor of several scientific journals,


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a reviewer for a number of funding agencies, and an advisor for a number of scientific initiatives, as outlined above.

UCSF CAMPUSWIDE 2003 - present Ad hoc Faculty reviews (~30)

2003 - 2003 Future of Computing at UCSF Committee

2003 - 2007 MD/PhD Scientist in QB3 Search Committee

2003 - 2005 Byers Hall (QB3) Building Committee

2003 - 2005 Pharmaceutical Sciences and Pharmacogenomics Graduate Program Admissions Committee

2003 - present Bioinformatics and Medical Informatics Graduate Program Executive Committee

2003 - 2004 Bioinformatics and Medical Informatics Graduate Program Admissions Committee

2003 - 2004 Biophysics Graduate Program Admissions Committee

2005 - present iPQB Curriculum committee

2005 - present iPQB Executive Committee

2005 - 2009 iPQB Admissions Committee

2004 - 2004 Chancellor's Council committee

2004 - 2004 Academic Information Technology Coordinator search committee

2004 - present QB3 Executive Committee

2005 - 2008 Basic Sciences Research Resources Oversight Committee

2005 - 2011 Rock Hall Governance Committee

2005 - 2006 QB3 Governance/Community Committee, Chair

2005 - 2009 Mission Bay leadership committee

2006 - present Faculty steering committee for the shared computer cluster at QB3, Chair

2003 - 2004 Bioinformatics and Computational Biology Faculty Search Committee, Co-Chair

2005 - 2010 Systems Biology Faculty Search Committee

2005 - 2008 Systems Biology HHMI/NIBIB Training Grant Leadership Committee

2007 - present BMI Training Grant Leadership Committee

2007 - 2007 Quantitative Imaging Faculty Search Committee


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2008 - 2008 Human Genetics Faculty Search Committee, Co-Chair

2011 - 2011 Pharmacometrics Faculty Search Committee

2011 - present Bioinformatics Task Force

2011 - present IT Governance Committee on Research Technology

2012 - present Enabling Technologies Advisory Committee

2012 - 2012 Gladstone Institute Faculty Search Committee

2012 - present ICHS Infrastructure Committee

2012 - present Funding Shared Equipment Awards Committee

2012 - present Bioimaging Faculty Search Committee

2013 - present Data Center Services Advisory Board

2013 - present 2.0-Ideation for the Future of UCSF Committee

2013 - present Shared Research Facilities Roadmap Steering Committee

2014 - present Institute for Neurodegenerative Diseases Faculty Search Committee, Co-Chair

2015 - present Chair, QB3 Shared Cluster Steering Committee

2016 - present Basic Research - IT interactions committee

2016 - present Executive Committee of Institute for Computational Health Sciences (ICHS)

SCHOOL OF PHARMACY 2003 - 2008 SOP Information Technology Committee

2005 - 2005 SOP Strategic Planning Committee

2007 - 2007 SOP Advisory committee for sharing software royalties

2007 - 2007 SOP Advisory committee for developing the SOP price / performance metric

2007 - 2007 SOP Space allocation committee

2009 - present SOP Outreach to industry program

2010 - 2011 SOP Faculty Awards Committee

2012 - 2014 SOP Educational Policy Committee

2014 - present SOP Frontiers in Science and Practice of Therapeutics Committee

2015 - present Associate Dean of Research

2015 - present SOP leadership group


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DEPARTMENTAL SERVICE 2003 - present BTS Internal Advisory Committee

2013 - present PSPG Graduate Program Admissions Committee

TEACHING AND MENTORING

TEACHING SUMMARY When I arrived to UCSF in January 2003, I joined Prof. Patsy Babbit in leading the graduate and professional students' courses in Bioinformatics (BMI-206 and BPS-114). In 2008-09, I took the primary responsibility for these two courses. I also gave many of the lectures and supervised student activity associated with the courses (eg, student seminars, exercise sets). Since 2010, I contribute several lectures to BMI-206, but the course is led by others (BPS-114 does not exist anymore). I also participate as a guest lecturer in a number of other courses, such as Macromolecules and Chem 204. Since 2014, I began to be increasingly involved in BPS-134, a course for pharmacy students, led by Nancy Sambol. Finally, I am involved in the shaping of the curriculum for the graduate programs in the iPQB umbrella program, as a member of the iPQB curriculum committee and a contributor to the training grant re-submissions.

FORMAL TEACHING Academic Yr Course No. & Title Teaching Contribution School Class

Size

2004 - 2004 Bioinformatics BMI-206

Co-Organizer, Lecturer 15



2005 - 2005 Bioinformatics BPS-114















Organizer, Lecturer 15


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Academic Yr Course No. & Title Teaching Contribution School Class Size






Lecturer 130




Lecturer 15


Lecturer 15

2013 - 2013 BPS 134 Lecturer 6

2013 - 2013 NSF Proposal Course Lecturer

2014 - 2014 NSF Proposal Course Lecturer


Lecturer 15

2014 - 2014 BPS 134 Lecturer 6

2003 - present

Macromolecular Interactions BP-204

Occasional Guest Lecturer 20

2011 - present

Chem 204 Guest Lecturer 3

2015 - present

Systems Pharmacology, Pharmacogenomics 245B

Guest Lecturer 15

2015 - 2015 BPS 134 Lecturer 6

2016 - 2016 BPS 134 Lecturer 10

2017 - 2017 BPS 134 Lecturer 10

2018 - 2018 BPS 134 Lecturer 10

MENTORING SUMMARY I have been involved in both formal and informal teaching at UCSF, as illustrated by my contributions to the graduate courses, professional courses, and mentoring of students and postdocs in my laboratory, detailed in the corresponding sections of this cv.


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PREDOCTORAL STUDENTS SUPERVISED OR MENTORED Dates Name Program or

School Mentor Type Role Current

Position

1995 - 2000 Roberto Sanchez

Rockefeller University

PhD Advisor Associate Professor, Mount Sinai School of Medicine, NY

1999 - 2001 Eric Feyfant Rockefeller University

PhD Advisor Senior Scientist, Wyeth Inc. Cambridge, MA.

1999 - 2003 Nebojsa Mirkovic

Rockefeller University

PhD Advisor Postdoctoral fellow with Diana Murray at Weill Medical College of Cornell University, NY

2000 - 2003 Bino John Rockefeller University

PhD Advisor Assistant Professor, University of Pittsburg

2002 - 2008 Ranyee Chiang BMI PhD Advisor Postdoc at New York University

2003 - 2007 Fred Davis Biophysics PhD Advisor Postdoc at Janelia Farm, HHMI

2003 - 2008 Michael Kim BMI PhD Advisor The Mechanical Zoo

2003 - 2008 Libusha Kelly BMI PhD Advisor Postdoc at MIT, with Penny Chisholm

2004 - 2008 David Eramian Biophysics PhD Advisor Patent Counsel, eBay Inc.


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Dates Name Program or School

Mentor Type Role Current Position

2005 - 2008 Mark Peterson BMI PhD Advisor The Boston Consulting Group

2006 - 2011 David Barkan BMI PhD Advisor Staff Scientist, Protaganist Therapeutics

2006 - 2011 Keren Lasker Tel-Aviv University

PhD Advisor Postdoctoral Fellow, Stanford UniversityWolfson

2007 - 2009 Adam Marko BMI MSc Advisor Asuragen, Inc., Austin, TX Bioinformatics Developer

2007 - 2012 Jeremy Phillips BMI PhD Advisor Bioinformatics Analyst, Genome Institute/LBL

2009 - 2014 Peter Cimermancic

BMI PhD Advisor UCSF Specialist

2011 - 2015 Natalia Khuri Biophysics PhD Advisor Educational Program Director, UCSF-Stanford CERSI Lecturer,

2010 - 2016 Charles Greenberg

BMI PhD Advisor Lumiata, Inc of San Mateo, CA

2012 - present Adrian Stecula PSPG PhD Advisor Graduate Student

2012 - 2016 Sara Calhoun Biophysics PhD Advisor Lawrence Berkeley National Lab


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Dates Name Program or School

Mentor Type Role Current Position

2014 - present Ilan Chemmama

Biophysics PhD Advisor Graduate Student

2015 - present Seth Axen Biophysics PhD Advisor Graduate Student

POSTDOCTORAL FELLOWS AND RESIDENTS MENTORED Dates Name Fellow Mentor Role Faculty Role Current

Position

1995 - 1997 Ilya Vakser Postdoc researcher

Research supervision Professor, University of Kansas, Lawrence, KS

1996 - 1999 Azat Badretdinov

Postdoc researcher

Research supervision Senior scientific programmer at Accelrys Inc., San Diego

1997 - 2002 Andras Fiser Postdoc researcher

Research supervision Associate Professor, Albert Einstein College of Medicine, Bronx, NY

1998 - 2001 Francisco Melo Postdoc researcher

Research supervision Associate Professor, Pontificia Universidad Catolica de Chile

1999 - 2003 Ash Stuart Postdoc researcher

Research supervision Assistant Professor, Ramapo College, Mahwah, NJ


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Dates Name Fellow Mentor Role Faculty Role Current Position

1999 - 2006 Marc Marti-Renom

Adjunct Assistant Professor

Research supervision Assistant Professor, Prince Felipe Research Center, Valencia, Spain

2000 - 2002 Valya Ilyin Scientific Programmer

Research supervision Associate Professor, Northeastern University, Boston

2000 - 2006 Andrea Rossi Postdoc researcher

Research supervision Senior Scientist, Rinat Laboratories, Pfizer Inc.

2000 - 2007 M.S. Madhusudhan

Postdoc researcher

Research supervision Assistant Professor, Bioinformatics Insitute, Singapore

2000 - 2008 Narayanan Eswar

Scientific Programmer

Research supervision Group Leader, Du Pont Inc.

2000 - 2014 Ursula Pieper Scientific Programmer

Research supervision Web Applications Specialist, National Agricultural Library

2001 - 2007 Frank Alber Postdoc researcher

Research supervision Assistant Professor, University of Southern California


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2002 - 2003 Bozidar Yerkovich

Scientific Programmer

Research supervision Head of Structural Bioinformatics at Rosetta Inpharmatics Inc., Seattle

2002 - 2006 Damien Devos Postdoc researcher

Research supervision Senior postdoc with Rob Russell, EMBL, Heidelberg

2002 - 2007 Dmitry Korkin Postdoc researcher

Research supervision Assistant Professor, University of Missouri at Columbia

2003 - 2004 Niu Huang Postdoc researcher

Research supervision Assistant Professor, Beijing, China

2003 - 2006 Maya Topf Postdoc researcher

Research supervision Lecturer, Department of Crystallography, Birkbeck College, London

2003 - 2006 Rachel Karchin Postdoc researcher

Research supervision Assistant Professor, Johns Hopkins University

2003 - 2008 Min-yi Shen Postdoc researcher

Research supervision Postdoc researcher

2003 - present Ben Webb Scientific Programmer

Research supervision Scientific Programmer

2005 - 2008 Friedrich Foerster

Postdoc researcher

Research supervision Postdoc researcher


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2006 - 2013 Javier Velazquez

Postdoc researcher

Research supervision Cypher Genomics Bioinformatics Analyst

2006 - 2014 Hao Fan Postdoc researcher

Research supervision A*STAR, Singapore Principal Investigator

2007 - 2014 Daniel Russel Postdoc researcher

Research supervision AltSchool Senior Research Engineer

2008 - 2012 Avner Schlessinger

Postdoc researcher

Research supervision Mount Sinai School of Medicine Assistant Professor

2008 - 2015 Dina Schneidman

Postdoc researcher

Research supervision Specialist

2008 - present Seung-Joong Kim

Postdoc researcher

Research supervision Specialist

2009 - 2011 Sebnem Essiz Postdoc researcher

Research supervision Assistant Professor, Kadir Has University, Istanbul

2009 - 2014 Guangqiang Dong

Postdoc researcher

Research supervision Data Scientist, Facebook

2009 - 2014 Patrick Weinkam

Postdoc researcher

Research supervision Lead Engineer, Data Science, Baselayer

2009 - present Elina Tjioe Scientific Programmer

Research supervision Scientific Programmer


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2010 - 2011 Backy Chen Postdoc researcher

Research Supervision Institute of Biomedical Science, Academia Sinica, Taiwan, Postdoc Researcher

2010 - 2013 Massimiliano Bonomi

Postdoc researcher

Research Supervision Postdoc researcher

2010 - present Riccardo Pellarin

Postdoc researcher

Research Supervision Postdoctoral Fellow, Institut Pasteur

2011 - 2012 Lan Hua Postdoc researcher


2012 - 2013 Miriam Sgobba Postdoc researcher


2012 - present Barak Raveh Postdoc researcher


2014 - 2016 Peter Cimermancic

Postdoc researcher

Research Supervision Specialist

2014 - present Shruthi Viswanath

Postdoc researcher


2014 - present Kate Stafford Postdoc researcher


2014 - present Daniel Saltzberg

Postdoc researcher


2015 - present Ignacia Echeverria

Postdoc researcher


2016 - present Sai Ganesan Postdoc researcher

Research Supervisor Postdoc researcher

2016 - present Nikita Chopra Postdoc researcher


2017 - present Kala Pilla Postdoc researcher



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2017 - present Jeremy Tempkin

Postdoc researcher


2017 - present Rakesh Ramachandran

Postdoc researcher

Research/Scholarly Mentor


2018 - present Leah Ray Postdoc researcher


FACULTY MENTORING Dates Name Position while

Mentored Mentor Type Mentoring Role Current

Position

2013 - present Sourav Bandyopadhyay

Assistant Professor

Mentor Assistant Professor, BTS

2012 - present Graham Johnson

Fellow Mentor QB3 Fellow, BTS

2010 - present Ryan Hernandez

Assistant Professor


2011 - present Rada Savic Assistant Professor


2004 - 2013 Tanja Kortemme

Assistant Professor

Mentor Professor, BTS

2007 - 2008 Mats Gustafsson

Assistant Professor

Mentor Assistant Professor, Physiology

RESEARCH AND CREATIVE ACTIVITIES

RESEARCH AND CREATIVE ACTIVITIES SUMMARY I have a broad background in computational structural biology, with the emphasis on structural modeling and simulations: I have developed and applied methods for comparative protein structure modeling, functional annotation of proteins, and integrative structure determination of macromolecular assemblies, as well as contributed to the understanding of the protein folding process. For example, in the field of protein structure prediction, I introduced homology or comparative modeling by satisfaction of spatial restraints, which utilizes both physical and statistical information, thereby improving its accuracy and applicability. The corresponding program, MODELLER, has been licensed to over 50,000 academic users, as well as many pharmaceutical groups, and is perhaps the most widely used program for comparative modeling. The resulting database of models for approximately 6 million known protein sequences, ModBase, is linked bi-directionally to a number of key biological databases,


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including UniProt. My major current research objective is to develop and apply a computational system for enumerating structures of protein assemblies that are consistent with all available information from experimental methods, physical theories, and statistical inference. Such an integrative system will maximize efficiency, accuracy, resolution, and completeness of the structural coverage of macromolecular assemblies. The current version of the corresponding program, Integrative Modeling Platform (IMP), is being used to determine the structures of a number of macromolecular assemblies, in collaboration with experimentalists. Most prominently, the approach already enabled the determination of the configuration of the 456 proteins in the yeast Nuclear Pore Complex and 19 proteins in the 19S subunit of the 26S proteasome. 1. Integrative structural biology. Samples of many biological macromolecules prove recalcitrant to mainstream structural biology methods. In such cases, structures can often be determined by consideration of complementary information from multiple methods. Thus, we are developing mathematical formalism and open source computer software for enumerating structures of macromolecular assemblies that are consistent with all available information from experimental methods, physical theories, and statistical preferences extracted from biological databases (IMP; http://integrativemodeling.org). To achieve this objective, we formulated the problem as an optimization task, requiring a hierarchical representation of the modeled system, a scoring function that incorporates input information, and a sampling scheme that finds good scoring solutions. The integrative approach facilitates maximizing the accuracy, precision, completeness, and efficiency of the structural coverage of biomolecular systems. In addition, we are contributing to the nucleation of the scientific community concerned with computation, validation, visualization, archival, and dissemination of integrative structures, in part through several advisory groups associated with the Protein Data Bank, Keystone Symposia SAB, and editing of Structure. F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni, R. Williams, B.T. Chait, M.P Rout, A. Sali. “Determining the architectures of macromolecular assemblies.” Nature 450, 683-694, 2007. PMID: 18046405 F. Alber, F. Förster, D. Korkin, M. Topf, A. Sali. “Integrating Diverse Data for Structure Determination of Macromolecular Assemblies.” Ann Rev Biochem 77, 443-477, 2008. PMID: 18318657 F. Forster, B. Webb, K.A. Krukenberg, H. Tsuruta, D.A. Agard, A. Sali. "Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies." J Mol Biol 382, 1089-1106, 2008. PMCID: PMC2745287 Russel D, Lasker K, Webb B, Velazquez-Muriel J, Tjioe E, Schneidman-Duhovny D, Peterson B, Sali A. Putting the pieces together: integrative structure determination of macromolecular assemblies. PLoS Biol 10, e1001244, 2012. PMCID: PMC3260315 2. Determining structures of macromolecular assemblies. It is essential for developers of computational methods to collaborate with experimentalists in applying their methods to practical problems. Such applications provide a validation of the methods as well as feedback for further development. Since 2001, we applied our integrative structure determination approach to over 20 macromolecular assemblies, exemplified by the four papers listed below. The resulting structures often facilitated insights into their evolution, function, and modulation. C.M. Spahn, R. Beckmann, N. Eswar, P.A. Penczek, A. Sali, G. Blobel, J. Frank. "Structure of the 80S ribosome from Saccharomyces cerevisiae tRNA-ribosome and subunit-subunit interactions." Cell 107, 373-386, 2001. PMID: 11701127


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F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni, R. Williams, B.T. Chait, A. Sali, M.P. Rout. “The Molecular Architecture of the Nuclear Pore Complex.” Nature 450, 695-701, 2007. PMID: 18046406 Lasker K, Forster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci USA 109, 1380-1387, 2012. PMCID: PMC3277140 J. Erzberger, F. Stengel, R. Pellarin, S. Zhang, T. Schaefer, C. Aylett, P. Cimermancic, D. Boehringer, A. Sali, R. Aebersold, N. Ban. "Molecular architecture of the 40S•eIF1•eIF3 translation initiation complex." Cell 158, 1125-1135, 2014. PMCID: PMC4151992 3. Development of comparative protein structure modeling. The accuracy of homology or comparative modeling is limited by the information that can be used in model calculations. Thus, we introduced comparative modeling by satisfaction of spatial restraints, which utilizes both physical and statistical information, thereby improving its accuracy and applicability. The corresponding program, MODELLER, has been distributed to over 50,000 academic users as well as many pharmaceutical groups, and is perhaps the most widely used program for comparative modeling. Because the genomic scale of biological data sets and accessibility require automation, we improved and implemented the entire process of comparative modeling, including fold assignment, sequence-structure alignment, model building, and model assessment, allowing us to calculate useful models for domains in ~65% of all known protein sequences. The resulting database, ModBase, is linked bi-directionally to UniProt at EBI and several other major biological databases. Our comparative modeling results led us to suggest some key aspects of the target selection strategies for the structural genomics initiative. A. Sali, T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234, 779-815, 1993. PMID: 8254673 A. Fiser, R.K.G. Do, A. Sali. "Modeling of loops in protein structures." Protein Sci 9, 1753-1773, 2000. PMID: 11045621 B. John, A. Sali. "Comparative protein structure modeling by iterative alignment, model building and model assessment." Nucleic Acids Res 31, 3982-3992, 2003. PMID: 12853614 M.-Y. Shen, A. Sali. “Statistical Potential for Assessment and Prediction of Protein Structure” Protein Science 15, 2507-2524, 2006. PMID: 17075131 4. Development of methods for annotation of protein function. We have contributed a number of concepts, methods, programs, web servers, and databases in the bioinformatics toolbox for structure-based functional annotation of proteins (http://salilab.org). Examples include a machine-learning method for predicting functional consequences of single point mutations in proteins, optimized protocols for virtual screening against comparative models, various methods for predicting functional sites and localizing cryptic sites on protein structures, as well as databases of protein-protein interfaces and protein-small molecule interactions. To maximize our impact, we are also applying these tools in collaboration with biologists. An example is our extensive characterization of ABC and SLC membrane transporters, including mapping their evolution by classification, identification of their ligands by virtual screening and experimental validation, and prediction of functional impact of their point mutants; these studies contributed to structural genomics of ABC and SLC transporters. R. Karchin, M. Diekhans, L. Kelly, D.J. Thomas, U. Pieper, N. Eswar, D. Haussler, A. Sali. "LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources." Bioinformatics 21, 2814-2820, 2005. PMID: 15827081


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F.P. Davis, A. Sali. "PIBASE: a comprehensive database of structurally defined protein interfaces." Bioinformatics 21, 1901-1907, 2005. PMID: 15657096 A. Schlessinger, E. Geier, H. Fan, J. Irwin, B. Shoichet, K. Giacomini, A. Sali. "Structure-based Discovery of Prescription Drugs that Interact with the Norepinephrine Transporter, NET." Proc Natl Acad Sci USA 108, 15810-15815, 2011. PMID: 21885739 U. Pieper, B. Webb, G.Q. Dong, D. Schneidman-Duhovny, H. Fan, S.J. Kim, N. Khuri, Y. Spill, P. Weinkam, M. Hammel, J. Tainer, M. Nilges, A. Sali. "ModBase, a database of annotated comparative protein structure models, and associated resources." Nucleic Acids Res 42, 336-346, 2014. PMCID: PMC3965011 5. Insights into protein folding and allostery. We used a simple 3D lattice model of a protein chain to contribute to the current view of protein folding, which suggests that proteins can often fold via an ensemble of pathways, not a single one. Simulations suggested that the necessary and sufficient condition for a sequence to fold rapidly was a pronounced energy minimum for the native state. This finding was explained by an elementary, three-stage random search mechanism of folding. The rate-limiting step was a random search by local chain rearrangement in the semi-compact part of the phase space; a resolution of the Levinthal paradox without recourse to a folding pathway was made possible by a sufficiently small ratio between the numbers of states in the semi-compact and transition regions. The pronounced energy minimum of a folding sequence allowed the search to take place at a temperature that was high enough for the chain to rearrange efficiently, but also low enough for the native state to remain thermodynamically stable. More recently, we used realistic multi-minima Gõ models to simulate allostery at atomic resolution, and predict impact of point mutations on the allostery mechanism. A. Sali, E. Shakhnovich, M. Karplus. "How does a protein fold?" Nature 369, 248-251, 1994. PMID: 7710478 A. Sali, E. Shakhnovich, M. Karplus. "Kinetics of protein folding. A lattice model study of the requirements for folding to the native state." J Mol Biol 235, 1614-1636, 1994. PMID: 8107095 P. Weinkam, J. Pons, A. Sali. "Structure-based Model of Allostery Predicts Coupling Between Distant Sites." Proc Natl Acad Sci USA 109, 4875-4880, 2012. PMCID: PMC3324024 P. Weinkam, Y.C. Chen, J. Pons, A. Sali. "Impact of mutations on the allosteric conformational equilibrium." J Mol Biol 425, 647-661, 2013. PMCID: PMC3557769

RESEARCH AWARDS - CURRENT 1. P41 GM109824 Co-Investigator Rout (PI) NIH 08/01/2014 04/30/2019 National Center for Dynamic Interactome Research $ 189,269 direct/yr

1 $ 995,000 total

The central goal of the proposed National Center for Dynamic Interactome Research (NCDIR) is to address the urgent need for technologies that can rapidly, reliably and routinely reveal and interpret the dynamic cellular interactome.

2. P01 GM105537 Co-Investigator Winey (PI) NIH 09/01/2014 08/31/2019 The Yeast Centrosome-Structure, Assembly &

Function $ 135,000 direct/yr 1

$ 750,000 total

The goal of this project is to understand the structure and function of centrosomes.


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3. P01AG002132 Co-Investigator Prusiner (PI) NIH 6/16/2015 03/31/2020 Degenerative and Dementing Diseases of Aging $ 140,000 direct/yr

1 $ 700,000 total

The central goal is mapping protein self-assemblies that lead to a number of neurodegenerative and systemic disorders.

4. R01GM112108 Co-Investigator Michael P. Rout

(PI) NIH 08/01/2014 02/28/2019 Structure-Function Mapping of the Nuclear Pore

Complex $ 48,000 direct/yr 1

$ 192,000 total

The goal is to construct a model of the transport through the Nuclear Pore Complex, based on varied theoretical considerations and experimental datasets.

5. P01 GM111126 Co-Investigator Stroud (PI) NIH 08/01/2015 07/31/2020 Mapping the conformational cycle of

transmembrane transporters $ 200,000 direct/yr 1

$ 1,000,000 total

The goal is to apply integrative structure determination to select ABC transporters. 6. R01 GM083960 PI Sali (PI) NIH/NIGMS 04/01/2017 03/31/2021 IMP: Software for Hybrid Determination of

Macromolecular Assembly Structures $ 220,000 direct/yr 1

$ 880,000 total

The goal is to develop and implement methods for integrative modeling of macromolecular assembly structures in the open source IMP package and to support its distribution.

7. U54DK107981 Co-Investigator Alber (PI) NIH/NIDDK Mapping the 3D Genome Landscape $ 79,701 direct/yr

1 $ 398,505 total

The aim is to upgrade IMP to allow for mapping the three-dimensional organization of the genome.

8. P01 GM118303 Co-Investigator Gerlt (PI) University of Illinois/NIH/NIGMS 04/01/2016 06/30/2021 Discovery of Microbial Metabolic Pathways Guided

by Ligand Binding $ 78,768 direct/yr 1


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Program project focuses on the development and application of novel computational and experimental strategies for the discovery of novel metabolic pathways in microbial species for which complete genome sequences are available.

9. R01GM117370 CoPi Taatjes (PI) NIH 01/01/2017 03/31/2018 Mediator kinases and transcription regulation $ 33,000 direct/yr

1

This collaborative project seeks to gain a deep mechanistic understanding of the Mediator kinases (CDK8 and CDK19) and the CDK8 module study CDK8 and CDK19 function in the context of serum response signaling, which is fundamentally important for cell physiology, development, and cancer biology.

10. HARC Webb (PI) HARC 09/01/2015 08/31/2018 Integrative Modeling of HIV-Human Protein

Complexes $ 63,046 direct/yr 1

Integrative Modeling of HIV-Human Protein Complexes

RESEARCH AWARDS - PAST 1. R01 GM54762 PI NIH/NIGMS 07/01/1996 06/30/2010 Protein Modeling by Satisfaction of Spatial Restraints $ 200,000

direct/yr 1 $ 2,500,000 total

2. U54 GM103511 Co-PI NIH/NIGMS 06/10/2005 07/31/2014 Nucliear Information Pathway Center $ 273,439

direct/yr 1 $ 2,100,000 total

3. P01 GM71790 Collaborator NIH/NIGMS 07/01/2004 06/30/2014 Deciphering Enzyme Specificity $ 96,350

direct/yr 1 $ 800,000 total

4. Sinsheimer Scholar Award PI Alexandrine and Alexander L. Sinsheimer Fund 09/01/1996 08/31/1998


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Knowledge-Based Protein Structure Modeling for Genome Projects

5. BIR-9601845 PI NSF 10/01/1996 09/30/1998 Acquisition of a Multiprocessor Computer for Computational

Physics and Structural Biology

6. Gift PI Molecular Simulations, Inc. 07/01/1998 07/01/1998 7. Alfred P. Sloan Fellowship PI Alfred P. Sloan Foundation 10/01/1998 9/30/2000 8. R01 HL63284 Collaborator NIH/NHLBI 09/01/1999 08/31/2003 Disruption and Expression of Mast Cell Protease Genes 9. Mathers Foundation Award PI Mathers Foundation 01/01/2000 12/31/2002 Comparative Annotation of Eukaryotic Genomes: From Gene

Detection to Protein Structure Modeling

10. Career Scientist Award PI Irma T. Hirschl Monique Weill-Caulier Trust 01/01/2000 12/31/2004 Comparative Protein Structure Modeling for Genomics 11. The Merck Genome Research

Institute Award PI

The Merck Genome Research Institute 02/01/2000 01/31/2002


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Database of Comparative Protein Structure Model for Genomics

12. R33 CA84699 Co-PI NIH/NCI 02/01/2000 01/31/2003 Target Selection for the Structural Genomics of Cancer 13. Gift PI Prospect Genomics, Inc. 07/01/2000 07/01/2000 14. U54 GM074945 Co-PI SGX/NIH 09/30/2000 08/31/2010 NYSGRC: A Large-Scale Center for the Protein Structure

Initiative $ 261,032 direct/yr 1

$ 2,700,000 total

15. R33 C89810 Collaborator NIH/NCI 06/01/2001 03/31/2004 Comprehensive Map of Cellular Protein Interactions 16. EDUD-7824-020257-US PI Sun Academic Equipment Grant 07/03/2001 07/03/2001 Development of an Integrated Software Environment for

High-Throughput Structural Biology and Automated Comparative Protein Structure Modeling

17. RGP67/2003 Co-PI Human Frontier Science Program Organization 07/01/2003 06/30/2006 3-D Reconstruction and Identification of Postsynaptic

Molecular Complexes Images by Electron Cryotomography


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18. Sandler Center for Basic Research in Parasitic Diseases

Collaborator

Sandler Family Supporting Foundation 07/01/2003 06/30/2010 Bioinformatics of Host-Pathogen Interactions 19. California Institute for

Quantitative Biomedical Research

PI

08/01/2003 07/31/2005 Towards a Comprehensive Map of Protein-Ligand

Interactions

20. SUR Equipment Award PI IBM, Inc. 08/03/2003 08/03/2003 Large-Scale Protein Structure Modeling and Ligand Docking 21. Equipment Award PI Intel, Inc. 09/15/2003 09/15/2003 Large-Scale Protein Structure Modeling and Ligand Docking 22. EIA-0324645 Co-PI NSF 11/01/2003 10/31/2006 Subnanometer Structure-Based Fold Determination of

Biological Complexes

23. Opportunity Award PI Sandler Program in Basics Sciences 02/15/2004 02/14/2006 Hierarchical Framework for Structural Biology 24. P01 AI035797 Core PI NIH/AI 07/01/2004 06/30/2009 Targeting Cysteine Proteases - Antiparasitic Chemotherapy


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25. IIS-0705196 PI NSF 08/01/2007 07/31/2009 Integrated Modeling of Biological Nanomachines 26. EF 0626651 Collaborator NSF 01/01/2008 10/31/2010 The PhyloFacts Phylogenomic Encyclopedia of Microbial

Protein Families $ 17,261 direct/yr 1

$ 35,387 total

27. Pfizer / QB3 Award PI Pfizer, Inc. 09/01/2008 08/31/2009 Epitope Mapping by Combining Protein-Protein Docking and

Varied Low-Resolution Structural Data

28. S10 RR027100-01 PI NIH/NIGMS 04/01/2010 03/31/2011 High Perfomance Computing Cluster for Bioimaging and

Computational Biology $ 499,512 direct/yr 1

29. Pfizer, Inc. PI California Institute for Quantitative Biosciences (QB3) 07/01/2010 06/30/2011 A Computational Model of Allostery with Application to

Antibody Design $ 70,000 direct/yr 1

$ 70,000 total

30. PN2 EY016525 Co-PI NIH 09/30/2005 09/29/2011 Center for Protein Folding Machinery $ 50,000


31. SP41 RR001081-32S1 Collaborator NIH 09/15/2009 09/14/2011


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Resource for Biocomputing, Visualization, and Informatics $ 7,140 direct/yr 1

$ 14,500 total

32. PI Pfizer, Inc. 10/01/2013 09/30/2014 A Computational Model of Allostery with Application to

Antibody Design $ 55,000 direct/yr 1

$ 55,000 total

33. PI Bayer Inc. 12/15/2012 12/15/2014 Modeling of ternary MHCII-peptide-TCR complexes $ 73,877


34. U01 GM61390 Collaborator NIH/NIGMS 04/01/2003 06/30/2015 Pharmacogenetics of Membrane Transporters $ 45,000


35. U54 GM0094625 Co-PI NIH/NIGMS 07/01/2005 06/30/2015 CSMP: Centers for Membrane Protein Structure

Determination $ 65,000 direct/yr 1

$ 650,000 total

36. U54 GM093342 Co-PI NIH/NIGMS 04/01/2010 04/30/2015 Collaborative Center for an Enzyme Function Initiative $ 170,000


37. U01 GM098256 Co-PI NIH/NIGMS 07/01/2011 07/31/2015 Nucleocytoplasmic Transport: A Target for Cellular Control $ 50,000



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38. U54 GM094662 Co-PI NIH/NIGMS 07/01/2010 06/30/2015 New York Structural Genomics Research Consortium $ 150,000


39. R21 coPI Charly Craik

(PI) NIH 4/1/2014 3/31/2016 Extracellular Proteolysis as a Molecular Stratification Tool for

Cancer $ 20000 direct/yr 1

$ 40000 total

The goal is to apply machine learning to cancer proteolysis data sets. 40. PI Andrej Sali

(PI) QB3 1/1/2014 12/31/2015 Small molecular activators of the 20S proteasome $ 125000

direct/yr 1 $ 225000 total

The goal is to find small molecules that activate the human 20S proteasome. 41. P01 AI09575 Co-PI Sali (PI) NIH/NIGMS 07/13/2011 06/30/2016 Protein Homeostasis Mechanism Underlying Enterovirus

Replication and Evolution $ 130,000 direct/yr 1

$ 650,000 total

42. S10OD021596 PI Sali (PI) NIH 07/01/2016 06/30/2017 High Performance Computer for Computational Biosciences $ 443,460


Equipment grant for high performance computer for computational bioscience.

PEER REVIEWED PUBLICATIONS 1. M. Renko, A. Sali, V. Turk, M. Pokomy, I. Kregar. "A neutral metalloproteinase from

Streptomyces rimosus." Vestnik Slovenskega Kemijskega Drustva 32/2, 161-173, 1985.

2. B. Lenarcic, A. Ritonja, A. Sali, M. Kotnik, V. Turk, W. Machleidt. "Properties and structure of human spleen stefin B - a low molecular weight protein inhibitor of cysteine proteinases." In: Cysteine Proteinases and Their Inhibitors; First International Symposium, Portoroz, Yugoslavia, September 15-18, 1985. Xvi+846p. Ed: V. Turk, pp. 473-488, Walter De Gruyter and Co., Berlin, West Germany; New York, New York, USA., 1986.


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3. V. Turk, J. Brzin, B. Lenarcic, A. Sali, W. Machleidt. "Human stefins and cystatis: their properties and structural relationships." In: Cysteine Proteinases and Their Inhibitors; First International Symposium, Portoroz, Yugoslavia, September 15-18, 1985. Xvi+846p. Ed: V. Turk, pp. 429-442, Walter De Gruyter and Co., Berlin, West Germany; New York, New York, USA., 1986.

4. M. Kotnik, A. Sali, J. Kos, B. Turk, V. Turk. "Nova metoda za hitro dolocanje kineticnih konstant pri interakciji encima s kompetitivnim inhibitorjem (A new method for rapid determination of kinetic constants for competitive inhibition of enzymes)." Vestnik Slovenskaga Kemijskega Drustva 34, 369-377, 1987.

5. A. Sali, V. Turk. "Prediction of the secondary structures of stefins and cystatins, the low-molecular mass protein inhibitors of cysteine proteinases." Biol Chem Hoppe Seyler 368, 493-499, 1987.

6. T. Lah, I. Kregar, A. Sali, B. Lenarcic, M. Kotnik, V. Kostka, V. Turk. "Circular dichroism studies of different aspartyl proteinases and their interactions with pepstatin." Periodicum Biologorum 90, 31-38, 1988.

7. V. Turk, R. Jerala, B. Lenarcic, A. Sali. "Structural and functional aspects of human cathepsins B." In: Intracellular Proteolysis: Mechanisms and Regulations. Ed: N. Katunuma, E. Kominami, pp. 27 -37, Japan Scientific Societies Press, Berlin, West Germany; New York, New York, USA., 1989.

8. A. Sali, B. Veerapandian, J.B. Cooper, S.I. Foundling, D.J. Hoover, T.L. Blundell. "High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme." Embo Journal 8, 2179-2188, 1989.

9. T.L. Blundell, G. Elliott, S.P. Gardner, T. Hubbard, S. Islam, M. Johnson, D. Mantafounis, P. Murrayrust, J. Overington, J.E. Pitts, A. Sali, B.L. Sibanda, J. Singh, M.J.E. Sternberg, M.J. Sutcliffe, J.M. Thornton, P. Travers. "Protein engineering and design." Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 324, 447-460, 1989.

10. T.L. Blundell, D. Carney, T. Hubbard, M.S. Johnson, A. McLeod, J.P. Overington, A. Sali, M.S. Sutcliffe, P. Thomas. "Knowledge-based protein modelling and design." In: Advances in Protein Design: International Workshop 1988 GBF Monographs. Ed: H. Bloecker, J. Collins, R.D. Schmid, D. Schomburg, 12, pp. 39-43, VCH, London, UK, 1989.

11. A. Sali, T.L. Blundell. "Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming." J Mol Biol 212, 403-428, 1990.

12. A. Sali, J.P. Overington, M.S. Johnson, T.L. Blundell. "From Comparisons of protein sequences and structures to protein modelling and design." Trends Biochem Sci 15, 235-240, 1990.

13. B. Veerapandian, J.B. Cooper, A. Sali, T.L. Blundell. "X-ray analyses of aspartic proteinases. III Three-dimensional structure of endothiapepsin complexed with a transition-state isostere inhibitor of renin at 1.6 A resolution." J Mol Biol 216, 1017-1029, 1990.

14. J. Overington, M.S. Johnson, A. Sali, T.L. Blundell. "Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction." Procedures in Biological Science 241, 132-145, 1990.


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15. J.P. Overington, M.S. Johnson, C. Topham, A. McLeod, A. Sali, Z.Y. Zhu, L. Sibanda, T.L. Blundell. "Applications of environment specific amino acid substitution tables to identification of key residues in protein tertiary structure." Curr Sci 59, 867-874, 1990.

16. M.S. Johnson, A. Sali, T.L. Blundell. "Phylogenetic relationships from three-dimensional protein structures." Methods Enzymol 183, 670-690, 1990.

17. M.S. Johnson, J.P. Overington, A. Sali. "Knowledge-based protein modelling: Human plasma kallikrein and human neutrophil defensin." In: Chemistry: Techniques Structure and Function. Ed: J.J. Vilafranca, pp. 567-574, Academic Press, Inc., London, 1990.

18. M.S. Johnson, J. Overington, A. Sali, Z. Zhu, D. Donnelly, P. Thomas, A. McLeod, R. Goold, C. Topham, T.L. Blundell. "From comparative structure analysis to protein engineering: Knowledge-based protein modelling and design." Fresenius Journal of Analytic Chemistry 337, 1-3, 1990.

19. T.L. Blundell, M.S. Johnson, J.P. Overington, A. Sali. "Knowledge-based protein modeling and the design of novel molecules." In: Protein design and the development of new therapeutics and vaccines. Ed: J.B. Hook, G. Poste, pp. 209-227, Plenum Press, New York, NY, 1990.

20. T.L. Blundell, J.B. Cooper, A. Sali, Z.Y. Zhu. "Comparisons of the sequences, 3-D structures and mechanisms of pepsin-like and retroviral aspartic proteinases." Adv Exp Med Biol 306, 443-453, 1991.

21. T.L. Blundell, J.B. Cooper, D. Donnelly, H. Driessen, Y. Edwards, F. Eisenmenger, C. Frazao, M. Johnson, K. Niefind, M. Newman, J. Overington, A. Sali, C. Slingsby, V. Nalini, Z.Y. Zhu. "Patterns of sequence variation in families of homologous proteins." In: Methods in Protein Sequence Analysis. Ed: H. Jornval, J.O. Hoog, A.M. Gustavsson, pp. 373-385, Birkhauser Verlag, Basel, Switzerland, 1991.

22. A. Sali, J.P. Overington, M.S. Johnson, T.L. Blundell. "From modelling homologous proteins to prediction of structure." In: Protein design and the development of new therapeutics and vaccines. Ed: J.M. Goodfellow, D.S. Moss, pp. 231-245, Ellis Horwood Ltd., LYNGBY, DENMARK, 1991.

23. A. Sali, B. Veerapandian, J.B. Cooper, D.S. Moss, T. Hofmann, T.L. Blundell. "Domain flexibility in aspartic proteinases." Proteins 12, 158-170, 1992.

24. B. Veerapandian, J.B. Cooper, A. Sali, T.L. Blundell, R.L. Rosati, B.W. Dominy, D.B. Damon, D.J. Hoover. "Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases." Protein Sci 1, 322-328, 1992.

25. Z.Y. Zhu, A. Sali, T.L. Blundell. "A variable gap penalty function and feature weights for protein 3-D structure comparisons." Protein Eng 5, 43-51, 1992.

26. J. Overington, D. Donnelly, M.S. Johnson, A. Sali, T.L. Blundell. "Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds." Protein Sci 1, 216-226, 1992.

27. M.S. Johnson, J.P. Overington, A. Sali, T.L. Blundell. "From the comparative analysis of proteins to similarity-based modelling." In: Computer Modelling of Biomolecular Processes. Ed: V.A. Ratner, N.A. Kolchanov, pp. 191-196, Nova Science Publishers, London, 1992.


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28. J.P. Overington, Z.Y. Zhu, A. Sali, M.S. Johnson, R. Sowdhamini, G.V. Louie, T.L. Blundell. "Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins." Biochem Soc Trans 21 ( Pt 3), 597-604, 1993.

29. A. Sali, T.L. Blundell. "Comparative protein modelling by satisfaction of spatial restraints." J Mol Biol 234, 779-815, 1993.

30. A. Sali, R. Matsumoto, H.P. McNeil, M. Karplus, R.L. Stevens. "Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan-binding regions and protease-specific antigenic epitopes." J Biol Chem 268, 9023-9034, 1993.

31. A. Sali, T. Blundell. "Comparative protein modeling by statisfaction of spatial restraints." In: Protein Structure by Distance Analysis. Ed: H. Bohr, S. Brunak, pp. 64-86, TECH UNIV DENMARK, CTR BIOL SEQUENCE ANAL, LYNGBY, DENMARK, 1994.

32. A. Sali, J.P. Overington. "Derivation of rules for comparative protein modeling from a database of protein structure alignments." Protein Sci 3, 1582-1596, 1994.

33. A. Sali, E. Shakhnovich, M. Karplus. "Kinetics of protein folding. A lattice model study of the requirements for folding to the native state." J Mol Biol 235, 1614-1636, 1994.

34. A. Sali, E. Shakhnovich, M. Karplus. "How does a protein fold?" Nature 369, 248-251, 1994.

35. A. Dinner, A. Sali, M. Karplus, E. Shakhnovich. "Phase diagram of a model protein derived by exhaustive enumeration of the conformations." J Chem Phys 101, 1444-1451, 1994.

36. M. Karplus, A. Sali. "Theoretical studies of protein folding and unfolding." Curr Opin Struct Biol 5, 58-73, 1995.

37. M. Karplus, A. Caflisch, A. Sali, E. Shakhnovich. "Protein dynamics: From the native to the unfolded state and back again." In: Modelling of Biomolecular Structures and Mechanisms. Ed: A.Pullmanet al, pp. 69-84, Kluwer Academic Publishers, London, 1995.

38. A. Sali. "MODELLER: Implementing 3D protein modeling." In: mc^2, 2, pp. 5, Molecular Simulations Inc., Totowa, NJ, 1995.

39. X.D. Wu, B. Knudsen, S.M. Feller, J. Zheng, A. Sali, D. Cowburn, H. Hanafusa, J. Kuriyan. "Structural basis for the specific interaction of lysine-containing proline-rich peptides with the amino-terminal SH3 domain of c-Crk." Structure 3, 215-226, 1995.

40. R. Matsumoto, A. Sali, N. Ghildyal, M. Karplus, R.L. Stevens. "Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans." J Biol Chem 270, 19524-19531, 1995.

41. A. Sali. "Comparative protein modeling by satisfaction of spatial restraints." Mol Med Today 1, 270-277, 1995.

42. A. Sali, E. Shakhnovich, M. Karplus. "Protein Folding Studied by Monte Carlo Simulations." In: Protein Folds: A Distance Based Approach. Ed: H. Bohr, S. Brunak, pp. 202-216, CRC Press Inc., LYNGBY, DENMARK, 1995.

43. A. Sali, E. Shakhnovich, M. Karplus. "Thermodynamics and kinetics of protein folding from lattice Monte Carlo simulations." In: DIMACS Series in Discrete Mathematics and Theoretical Computer Science. Ed: D. Shalloway, G. Xue, P. Pardalos, 23, pp. 199-213, American Mathematical Society, LYNGBY, DENMARK, 1995.


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44. A. Sali, L. Potterton, F. Yuan, H. van Vlijmen, M. Karplus. "Evaluation of comparative protein modeling by MODELLER." Proteins 23, 318-326, 1995.

45. A. Sali. "Modeling mutations and homologous proteins." Curr Opin Biotechnol 6, 437-451, 1995.

46. M. Karplus, A. Sali, E. Shakhnovich. "Kinetics of protein folding." Nature 373, 664-665, 1995.

47. Y. Sheng, A. Sali, H. Herzog, J. Lahnstein, S.A. Krilis. "Site-directed mutagenesis of recombinant human beta 2-glycoprotein I identifies a cluster of lysine residues that are critical for phospholipid binding and anti-cardiolipin antibody activity." J Immunol 157, 3744-3751, 1996.

48. N. Ghildyal, D.S. Friend, R.L. Stevens, K.F. Austen, C. Huang, J.F. Penrose, A. Sali, M.F. Gurish. "Fate of two mast cell tryptases in V3 mastocytosis and normal BALB/c mice undergoing passive systemic anaphylaxis: prolonged retention of exocytosed mMCP-6 in connective tissues, and rapid accumulation of enzymatically active mMCP-7 in the blood." The Journal of Experimental Medicine 184, 1061-1073, 1996.

49. L.Z. Xu, R. Sanchez, A. Sali, N. Heintz. "Ligand specificity of brain lipid-binding protein." J Biol Chem 271, 24711-24719, 1996.

50. A.R. Dinner, A. Sali, M. Karplus. "The folding mechanism of larger model proteins: role of native structure." Proc Natl Acad Sci U S A 93, 8356-8361, 1996.

51. S. Wu, H. de Lencastre, A. Sali, A. Tomasz. "A phosphoglucomutase-like gene essential for the optimal expression of methicillin resistance in Staphylococcus aureus: molecular cloning and DNA sequencing." Microbial Drug Resistance 2, 277-286, 1996.

52. M. Russel, N.A. Linderoth, A. Sali. "Filamentous phage assembly: variation on a protein export theme." Gene 192, 23-32, 1997.

53. C. Huang, G.W. Wong, N. Ghildyal, M.F. Gurish, A. Sali, R. Matsumoto, W.T. Qiu, R.L. Stevens. "The tryptase, mouse mast cell protease 7, exhibits anticoagulant activity in vivo and in vitro due to its ability to degrade fibrinogen in the presence of the diverse array of protease inhibitors in plasma." J Biol Chem 272, 31885-31893, 1997.

54. R. Sanchez, A. Sali. "Comparative protein modeling as an optimization problem." Journal of Molecular Structure (Theochem) 398, 489-496, 1997.

55. R. Sanchez, A. Sali. "Advances in comparative protein-structure modelling." Curr Opin Struct Biol 7, 206-214, 1997.

56. D. Koulich, M. Orlova, A. Malhotra, A. Sali, S.A. Darst, S. Borukhov. "Domain organization of Escherichia coli transcript cleavage factors GreA and GreB." J Biol Chem 272, 7201-7210, 1997.

57. J.E. Hunt, D.S. Friend, M.F. Gurish, E. Feyfant, A. Sali, C. Huang, N. Ghildyal, S. Stechschulte, K.F. Austen, R.L. Stevens. "Mouse mast cell protease 9, a novel member of the chromosome 14 family of serine proteases that is selectively expressed in uterine mast cells." J Biol Chem 272, 29158-29166, 1997.

58. R. Sanchez, A. Sali. "Evaluation of comparative protein structure modeling by MODELLER-3." Proteins Suppl 1, 50-58, 1997.


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59. B. Guenther, R. Onrust, A. Sali, M. O'Donnell, J. Kuriyan. "Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III." Cell 91, 335-345, 1997.

60. R. Sanchez, A.Ya. Badretdinov, E. Feyfant, A. Sali. "Homology protein structure modeling." Transactions of the American Crystallographic Association 32, 81-91, 1997.

61. Y. Sheng, S.A. Krilis, A. Sali. "Site-directed mutagenesis of recombinant human beta 2-glycoprotein I. Effect of phospholipid binding and anticardiolipin antibody activity." Ann N Y Acad Sci 815, 331-333, 1997.

62. C.M. Dobson, A. Sali, M. Karplus. "Protein folding: A perspective from theory and experiment." Angewandte Chemie Int Ed 37, 868-893, 1998.

63. C. Huang, A. Sali, R.L. Stevens. "Regulation and function of mast cell proteases in inflammation." J Clin Immunol 18, 169-183, 1998.

64. D.A. Kandiah, A. Sali, Y. Sheng, E.J. Victoria, D.M. Marquis, S.M. Coutts, S.A. Krilis. "Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects." Advanced Immunology Journal 70, 507-563, 1998.

65. A. Gutin, A. Sali, V. Abkevich, M. Karplus, E. Shakhnovich. "Temperature dependence of the folding rate in a simple protein model: Search for a glass transition." J Chem Phys 108, 6466-6483, 1998.

66. E. Wolf, A. Vassilev, Y. Makino, A. Sali, Y. Nakatani, S.K. Burley. "Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase." Cell 94, 439-449, 1998.

67. R. Sanchez, A. Sali. "Large-scale protein structure modeling of the Saccharomyces cerevisiae genome." Proc Natl Acad Sci U S A 95, 13597-13602, 1998.

68. A. Sali. "100,000 protein structures for the biologist." Nat Struct Biol 5, 1029-1032, 1998.

69. R. Sanchez, A. Sali. "MODBASE: A database of comparative protein structure models." Bioinformatics 15, 1060-1061, 1999.

70. R. Sanchez, A. Sali. "Comparative protein structure modeling in genomics." Journal of Computational Physics 151, 388-401, 1999.

71. G. Wu, A. Fiser, B. ter Kuile, A. Sali, M. Muller. "Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase." Proc Natl Acad Sci U S A 96, 6285-6290, 1999.

72. T. Nagata, V. Gupta, D. Sorce, W.Y. Kim, A. Sali, B.T. Chait, K. Shigesada, Y. Ito, M.H. Werner. "Immunoglobulin motif DNA recognition and heterodimerization of the PEBP2/CBF Runt domain." Nat Struct Biol 6, 615-619, 1999.

73. J.M. Miwa, I. Ibanez-Tallon, G.W. Crabtree, R. Sanchez, A. Sali, L.W. Role, N. Heintz. "lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS." Neuron 23, 105-114, 1999.

74. G.W. Wong, Y. Tang, E. Feyfant, A. Sali, L. Li, Y. Li, C. Huang, D.S. Friend, S.A. Krilis, R.L. Stevens. "Identification of a new member of the tryptase family of mouse and human mast cell proteases which possesses a novel COOH-terminal hydrophobic extension." J Biol Chem 274, 30784-30793, 1999.


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75. S.K. Burley, S.C. Almo, J.B. Bonanno, M. Capel, M.R. Chance, T. Gaasterland, D. Lin, A. Sali, F.W. Studier, S. Swaminathan. "Structural genomics: beyond the human genome project." Nat Genet 23, 151-157, 1999.

76. A. Sali, J. Kuriyan. "Challenges at the frontiers of structural biology (Reprinted from Trends in Biochemical Science, vol 12, Dec., 1999)." Trends Cell Biol 9, M20-M24, 1999.

77. A. Sali. "Functional links between proteins." Nature 402, 23, 25-26, 1999.

78. P. Baldi, M. Borodovsky, S. Brunak, C. Burge, J. Fickett, S. Henikoff, E. Koonin, A. Sali, C. Sander, G. Stormo. "The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function." Bioinformatics 15, 865-866, 1999.

79. C. Huang, G. Morales, A. Vagi, K. Chanasyk, M. Ferrazzi, C. Burklow, W.T. Qiu, E. Feyfant, A. Sali, R.L. Stevens. "Formation of enzymatically active, homotypic, and heterotypic tetramers of mouse mast cell tryptases. Dependence on a conserved Trp-rich domain on the surface." J Biol Chem 275, 351-358, 2000.

80. M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sanchez, F. Melo, A. Sali. "Comparative protein structure modeling of genes and genomes." Annu Rev Biophys Biomol Struct 29, 291-325, 2000.

81. R. Sanchez, U. Pieper, N. Mirkovic, P.I.W. de Bakker, E. Wittenstein, A. Sali. "ModBase, a database of annotated comparative protein structure models." Nucleic Acids Res 28, 250-253, 2000.

82. A.R. Dinner, A. Sali, L.J. Smith, C.M. Dobson, M. Karplus. "Understanding protein folding via free-energy surfaces from theory and experiment." Trends Biochem Sci 25, 331-339, 2000.

83. R. Sanchez, A. Sali. "Comparative protein structure modeling. Introduction and practical examples with modeller." Methods Mol Biol 143, 97-129, 2000.

84. G. Wu, A.G. McArthur, A. Fiser, A. Sali, M.L. Sogin, M. Muller. "Core histones of the amitochondriate protist, Giardia lamblia." Mol Biol Evol 17, 1156-1163, 2000.

85. A. Fiser, R.K.G. Do, A. Sali. "Modeling of loops in protein structures." Protein Sci 9, 1753-1773, 2000.

86. W. Liedtke, Y. Choe, M.A. Marti-Renom, A.M. Bell, C.S. Denis, A. Sali, A.J. Hudspeth, J.M. Friedman, S. Heller. "Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor." Cell 103, 525-535, 2000.

87. S.K. Jin, S. Martinek, W.S. Joo, J.R. Wortman, N. Mirkovic, A. Sali, M.D. Yandell, N.P. Pavletich, M.W. Young, A.J. Levine. "Identification and characterization of a p53 homologue in Drosophila melanogaster." Proc Natl Acad Sci U S A 97, 7301-7306, 2000.

88. R. Sanchez, U. Pieper, F. Melo, N. Eswar, M.A. Marti-Renom, M.S. Madhusudhan, N. Mirkovic, A. Sali. "Protein structure modeling for structural genomics." Nat Struct Biol 7, 986-990, 2000.

89. A. Fiser, R. Sanchez, F. Melo, A. Sali. "Comparative protein structure modeling." In: Computational Biochemistry and Biophysics. Ed: M. Watanabe, B. Roux, A. Mackerell, O. Becker, pp. 275-312, Marcel Dekker, Oxford, UK, 2000.

90. C.M. Groft, R. Beckmann, A. Sali, S.K. Burley. "Crystal structures of ribosome anti-association factor IF6." Nat Struct Biol 7, 1156-1164, 2000.


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91. S. Gopal, M. Schroeder, U. Pieper, A. Sczyrba, G. Aytekin-Kurban, S. Bekiranov, J.E. Fajardo, N. Eswar, R. Sanchez, A. Sali, T. Gaasterland. "Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome." Nat Genet 27, 337-340, 2001.

92. V.A. Eyrich, M.A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, A. Fiser, F. Pazos, A. Valencia, A. Sali, B. Rost. "EVA: continuous automatic evaluation of protein structure prediction servers." Bioinformatics 17, 1242-1243, 2001.

93. M.A. Marti-Renom, V.A. Ilyin, A. Sali. "DBAli: a database of protein structure alignments." Bioinformatics 17, 746-747, 2001.

94. G.W. Wong, L. Li, M.S. Madhusudhan, S.A. Krilis, M.F. Gurish, M.E. Rothenberg, A. Sali, R.L. Stevens. "Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases." J Biol Chem 276, 20648-20658, 2001.

95. L.G. Barrientos, R. Campos-Olivas, J.M. Louis, A. Fiser, A. Sali, A.M. Gronenborn. "1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N." J Biomol NMR 19, 289-290, 2001.

96. A. Sali. "Target practice." Nat Struct Biol 8, 482-484, 2001.

97. J.B. Bonanno, C. Edo, N. Eswar, U. Pieper, M.J. Romanowski, V. Ilyin, S.E. Gerchman, H. Kycia, F.W. Studier, A. Sali, S.K. Burley. "Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis." Proc Natl Acad Sci U S A 98, 12896-12901, 2001.

98. C.M. Spahn, R. Beckmann, N. Eswar, P.A. Penczek, A. Sali, G. Blobel, J. Frank. "Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions." Cell 107, 373-386, 2001.

99. R. Beckmann, C.M.T. Spahn, N. Eswar, J. Helmers, P.A. Penczek, A. Sali, J. Frank, G. Blobel. "Architecture of the protein-conducting channel associated with the translating 80S ribosome." Cell 107, 361-372, 2001.

100. G.W. Wong, S. Yasuda, M.S. Madhusudhan, L. Li, Y. Yang, S.A. Krilis, A. Sali, R.L. Stevens. "Human tryptase epsilon (PRSS22), a new member of the chromosome 16p13.3 family of human serine proteases expressed in airway epithelial cells." J Biol Chem 276, 49169-49182, 2001.

101. M. Borodovsky, E. Koonin, C. Burge, J. Fickett, J. Logsdon, A. Sali, G. Stormo, I. Zhulin. "The third Georgia Tech - Emory international conference on bioinformatics: in silico biology; bioinformatics after human genome November 15-18, 2001, Atlanta, Georgia, USA." Bioinformatics 17, 859-861, 2001.

102. C.M. Groft, R. Beckmann, A. Sali, S.K. Burley. "Response to Paoli." Nat Struct Biol 8, 745, 2001.

103. D. Baker, A. Sali. "Protein structure prediction and structural genomics." Science 294, 93-96, 2001.

104. J. Vernal, A. Fiser, A. Sali, M. Muller, J.J. Cazzulo, C. Nowicki. "Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis." Biochem Biophys Res Commun 293, 633-639, 2002.

105. F. Melo, R. Sanchez, A. Sali. "Statistical potentials for fold assessment." Protein Sci 11, 430-448, 2002.


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106. A.C. Stuart, V.A. Ilyin, A. Sali. "LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures." Bioinformatics 18, 200-201, 2002.

107. M.A. Marti-Renom, M.S. Madhusudhan, A. Fiser, B. Rost, A. Sali. "Reliability of assessment of protein structure prediction methods." Structure 10, 435-440, 2002.

108. A. Sali, M.A. Marti-Renom, M.S. Madhusudhan, A. Fiser, B. Rost. "Reply to Moult et al." Structure 10, 292-293, 2002.

109. A. Fiser, M. Feig, C.L. Brooks, A. Sali. "Evolution and physics in comparative protein structure modeling." Accounts of Chemical Research 35, 413-421, 2002.

110. U. Pieper, N. Eswar, A.C. Stuart, V.A. Ilyin, A. Sali. "MODBASE, a database of annotated comparative protein structure models." Nucleic Acids Res 30, 255-259, 2002.

111. M.R. Chance, A.R. Bresnick, S.K. Burley, J.S. Jiang, C.D. Lima, A. Sali, S.C. Almo, J.B. Bonanno, J.A. Buglino, S. Boulton, H. Chen, N. Eswar, G.S. He, R. Huang, V. Ilyin, L. McMahan, U. Pieper, S. Ray, M. Vidal, L.K. Wang. "Structural genomics: A pipeline for providing structures for the biologist." Protein Sci 11, 723-738, 2002.

112. K.R. Rajashankar, M.R. Chance, S.K. Burley, J. Jiang, S.C. Almo, A.R. Bresnick, T. Dodatko, R. Huang, G. He, H. Chen, M. Sullivan, J. Toomey, R.A. Thirumuruhan, W.A. Franklin, A. Sali, U. Pieper, N. Eswar, V. Ilyin, L. McMahan. "Structural Genomics at the National Synchrotron Light Source." NSLS Activity Report 2001 2, 28-32, 2002.

113. Y. Yang, L.X. Li, G.W. Wong, S.A. Krilis, M.S. Madhusudhan, A. Sali, R.L. Stevens. "RasGRP4, a new mast cell-restricted Ras guanine nucleotide-releasing protein with calcium- and diacylglycerol-binding motifs - Identification of defective variants of this signaling protein in asthma, mastocytosis, and mast cell leukemia patients and demonstration of the importance of RasGRP4 in mast cell development and function." J Biol Chem 277, 25756-25774, 2002.

114. M.A. Marti-Renom, B. Yerkovich, A. Sali. "Comparative protein structure prediction." In: Current Protocols in Protein Science, pp. 2.9.1-2.9.22, John Wiley & Sons, Totowa, NJ, 2002.

115. G.M. Iverson, S. Reddel, E.J. Victoria, K.A. Cockerill, Y.X. Wang, M.A. Marti-Renom, A. Sali, D.M. Marquis, S.A. Krilis, M.D. Linnik. "Use of single point mutations in domain I of beta(2)-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies." J Immunol 169, 7097-7103, 2002.

116. A. Fiser, A. Sali. "Modeller: generation and refinement of homology-based protein structure models." Methods Enzymol 374, 461-491, 2003.

117. V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, L. McMahan, A. Sali. "ModView, visualization of multiple protein sequences and structures." Bioinformatics 19, 165-166, 2003.

118. M.A. Marti-Renom, B. Yerkovich, A. Sali. "Modeling protein structure from its sequence." In: Current Protocols in Bioinformatics, V. 5 January Issue, pp. 5.1.1-5.1.32, John Wiley & Sons, Inc., Hoboken, NJ, Totowa, NJ, 2003.

119. A. Fiser, A. Sali. "Comparative Protein Structure Modeling." In: Protein Structure. Ed: D. Chasman, pp. 167-206, Marcel Dekker, Inc., Oxford, UK, 2003.


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120. A. Sali, R. Glaeser, T. Earnest, W. Baumeister. "From words to literature in structural proteomics." Nature 422, 216-225, 2003.

121. I.Y.Y. Koh, V.A. Eyrich, M.A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, N. Eswar, O. Grana, F. Pazos, A. Valencia, A. Sali, B. Rost. "EVA: evaluation of protein structure prediction servers." Nucleic Acids Res 31, 3311-3315, 2003.

122. B. John, A. Sali. "Comparative protein structure modeling by iterative alignment, model building and model assessment." Nucleic Acids Res 31, 3982-3992, 2003.

123. N. Eswar, B. John, N. Mirkovic, A. Fiser, V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, M.S. Madhusudhan, B. Yerkovich, A. Sali. "Tools for comparative protein structure modeling and analysis." Nucleic Acids Res 31, 3375-3380, 2003.

124. H.X. Gao, J. Sengupta, M. Valle, A. Korostelev, N. Eswar, S.M. Stagg, P. Van Roey, R.K. Agrawal, S.C. Harvey, A. Sali, M.S. Chapman, J. Frank. "Study of the structural dynamics of the E-coli 70S ribosome using real-space refinement." Cell 113, 789-801, 2003.

125. S.A. Lee, E.L. Shen, A. Fiser, A. Sali, S. Guo. "The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons." Development 130, 2669-2679, 2003.

126. M.A. Marti-Renom, A. Fiser, M.S. Madhusudhan, B. John, A.C. Stuart, N. Eswar, U. Pieper, M.-.Y. Shen, A. Sali. "Modeling protein structure from its sequence." In: Current Protocols in Bioinformatics, V. 5, pp. 5.1.1-5.1.32, John Wiley & Sons, Inc., Totowa, NJ, 2003.

127. A. Sali. "NIH workshop on structural proteomics of biological complexes." Structure 11, 1043-1047, 2003.

128. A. Fiser, A. Sali. "ModLoop: automated modeling of loops in protein structures." Bioinformatics 19, 2500-2501, 2003.

129. N. Mirkovic, M.A. Marti-Renom, B.L. Weber, A. Sali, A.N. Monteiro. "Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition." Cancer Res 64, 3790-3797, 2004.

130. A. Rossi, Q. Deveraux, B. Turk, A. Sali. "Comprehensive search for cysteine cathepsins in the human genome." Biol Chem 385, 363-372, 2004.

131. M.A. Marti-Renom, M.S. Madhusudhan, A. Sali. "Alignment of protein sequences by their profiles." Protein Sci 13, 1071-1087, 2004.

132. F. Alber, N. Eswar, A. Sali. "Structure determination of macromolecular complexes by experiment and computation." Practical Bioinformatics, Ed: J.Bujnicki 15, 73-96, 2004.

133. B. John, A. Sali. "Detection of homologous proteins by an intermediate sequence search." Protein Sci 13, 54-62, 2004.

134. S.M. Maurer, A. Rai, A. Sali. "Finding Cures for Tropical Diseases: Is Open Source An Answer?" Minnesota Journal of Law, Science & Technology 6, 169-175, 2004.

135. U. Pieper, N. Eswar, H. Braberg, M.S. Madhusudhan, F.P. Davis, A.C. Stuart, N. Mirkovic, A. Rossi, M.A. Marti-Renom, A. Fiser, B. Webb, D. Greenblatt, C.C. Huang, T.E. Ferrin, A. Sali. "MODBASE, a database of annotated comparative protein structure models, and associated resources." Nucleic Acids Res 32, D217-D222, 2004.


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136. S.M. Maurer, A. Rai, A. Sali. "Finding Cures for Tropical Diseases: Is Open Source An Answer?" In: Biotechnology: Essays From Its Heartland. Ed: L.y.n.n. Laboratory Yarris, June 2004, pp. 33-37, John Wiley & Sons, Totowa, NJ, 2004.

137. M.R. Chance, A. Fiser, A. Sali, U. Pieper, N. Eswar, G. Xu, J.E. Fajardo, T. Radhakannan, N. Marinkovic. "High-throughput computational and experimental techniques in structural genomics." Genome Res 14, 2145-2154, 2004.

138. M. Jacobson, A. Sali. "Comparative Protein Structure Modeling and Its Applications to Drug Discovery." In: Annual Reports in Medicinal Chemistry. Ed: J. Overington, 39, pp. 259-276, Inpharmatica Ltd., London, 2004.

139. R.B. Russell, F. Alber, P. Aloy, F.P. Davis, D. Korkin, M. Pichaud, M. Topf, A. Sali. "A structural perspective on protein-protein interactions." Curr Opin Struct Biol 14, 313-324, 2004.

140. D. Devos, S. Dokudovskaya, F. Alber, R. Williams, B.T. Chait, A. Sali, M.P. Rout. "Components of coated vesicles and nuclear pore complexes share a common molecular architecture." PLoS Biology 2, e380, 2004.

141. S.M. Maurer, A. Rai, A. Sali. "Finding Cures for Tropical Diseases: Is Open Source an Answer?" PLoS Medicine 1, e56, 2004.

142. J. Espadaler, R. Aragues, N. Eswar, M.A. Marti-Renom, E. Querol, F.X. Aviles, A. Sali, B. Oliva. "Detecting remotely related proteins by their interactions and sequence similarity." Proc Natl Acad Sci U S A 102, 7151-7156, 2005.

143. M. Topf, M.L. Baker, B. John, W. Chiu, A. Sali. "Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy." J Struct Biol 149, 191-203, 2005.

144. R. Karchin, L. Kelly, A. Sali. "Improving functional annotation of non-synonomous SNPs with information theory." Pac Symp Biocomput, 397-408, 2005.

145. M.S. Madhusudhan, M.A. Marti-Renom, N. Eswar, B. John, U. Pieper, R. Karchin, M.i.n.-.y.i. Shen, A. Sali. "Comparative Protein Structure Modeling." In: Proteomics Protocols Handbook. Ed: J.M. Walker, pp. 831-860, Humana Press Inc., Totowa, NJ, 2005.

146. F. Alber, M.F. Kim, A. Sali. "Structural characterization of assemblies from overall shape and subcomplex compositions." Structure 13, 435-445, 2005.

147. F.P. Davis, A. Sali. "PIBASE: a comprehensive database of structurally defined protein interfaces." Bioinformatics 21, 1901-1907, 2005.

148. R. Karchin, M. Diekhans, L. Kelly, D.J. Thomas, U. Pieper, N. Eswar, D. Haussler, A. Sali. "LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources." Bioinformatics 21, 2814-2820, 2005.

149. S. Yasuda, N. Morokawa, G.W. Wong, A. Rossi, M.S. Madhusudhan, A. Sali, Y.S. Askew, R. Adachi, G.A. Silverman, S.A. Krilis, R.L. Stevens. "Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22." Blood 105, 3893-3901, 2005.

150. J. Dvorak, M. Delcroix, A. Rossi, V. Vopalensky, M. Pospisek, M. Sedinova, L. Mikes, M. Sajid, A. Sali, J.H. Mckerrow, P. Horak, C.R. Caffrey. "Multiple cathepsin B isoforms in


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schistosomula of Trichobilharzia regenti: Identification, characterization and putative role in migration and nutrition." International Journal of Parasitology 35, 895-910, 2005.

151. A. Sali, W. Chiu. "Macromolecular assemblies highlighted." Structure 13, 339-341, 2005.

152. D. Korkin, F.P. Davis, A. Sali. "Localization of protein-binding sites within families of proteins." Protein Sci 14, 2350-2360, 2005.

153. M.Y. Shen, F.P. Davis, A. Sali. "The optimal size of a globular protein domain: A simple sphere-packing model." Chem Phys Lett 405, 224-228, 2005.

154. J.B. Bonanno, S.C. Almo, A. Bresnick, M.R. Chance, A. Fiser, S. Swaminathan, J. Jiang, F.W. Studier, L. Shapiro, C.D. Lima, T.M. Gaasterland, A. Sali, K. Bain, I. Feil, X. Gao, D. Lorimer, A. Ramos, J.M. Sauder, S.R. Wasserman, S. Emtage, K.L. D'Amico, S.K. Burley. "New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative." J Struct Funct Genom 6, 225-232, 2005.

155. M. Topf, A. Sali. "Combining electron microscopy and comparative protein structure modeling." Curr Opin Struct Biol 15, 578-585, 2005.

156. S.A. McMahon, J.L. Miller, J.A. Lawton, D.E. Kerkow, A. Hodes, M.A. Marti-Renom, S. Doulatov, E. Narayanan, A. Sali, J.F. Miller, P. Ghosh. "The C-type lectin fold as an evolutionary solution for massive sequence variation." Nature Structural Molecular Biology 12, 886-892, 2005.

157. D. Devos, S. Dokudovskaya, R. Williams, F. Alber, N. Eswar, B.T. Chait, M.P. Rout, A. Sali. "Simple fold composition and modular architecture of the nuclear pore complex." Proc Natl Acad Sci U S A 103, 2172-2177, 2006.

158. M.S. Madhusudhan, M.A. Marti-Renom, R. Sanchez, A. Sali. "Variable gap penalty for protein sequence-structure alignment." Protein Engineering, Design & Selection 19, 129-133, 2006.

159. C. Lima, J. Puglisi, A. Sali, L. Szewczak. "Editorial." Structure 14, 801, 2006.

160. U. Pieper, N. Eswar, F.P. Davis, H. Braberg, M.S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B.M. Webb, D. Eramian, M.Y. Shen, L. Kelly, F. Melo, A. Sali. "MODBASE: a database of annotated comparative protein structure models and associated resources." Nucleic Acids Res 34, D291-295, 2006.

161. M. Topf, M.L. Baker, M.A. Marti-Renom, W. Chiu, A. Sali. "Refinement of protein structures by iterative comparative modeling and CryoEM density fitting." J Mol Biol 357, 1655-1668, 2006.

162. D. Korkin, F.P. Davis, F. Alber, T. Luong, M.Y. Shen, V. Lucic, M.B. Kennedy, A. Sali. "Structural modeling of protein interactions by analogy: application to PSD-95." PLoS Computational Biology 2, e153, 2006.

163. D. Eramian, M.Y. Shen, D. Devos, F. Melo, A. Sali, M.A. Marti-Renom. "A composite score for predicting errors in protein structure models." Protein Sci 15, 1653-1666, 2006.

164. S. Dokudovskaya, R. Williams, D. Devos, A. Sali, B.T. Chait, M.P. Rout. "Protease accessibility laddering: a proteomic tool for probing protein structure." Structure 14, 653-660, 2006.


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165. N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper, A. Sali. "Comparative protein structure modeling using Modeller." Current Protocols in Bioinformatics Chapter 5, Unit 5.6, 2006.

166. A. Rossi, M.A. Marti-Renom, A. Sali. "Localization of binding sites in protein structures by optimization of a composite scoring function." Protein Sci 15, 2366-2380, 2006.

167. F.P. Davis, H. Braberg, M.Y. Shen, U. Pieper, A. Sali, M.S. Madhusudhan. "Protein complex compositions predicted by structural similarity." Nucleic Acids Res 34, 2943-2952, 2006.

168. T.D. Nguyen, J.M. Gow, L.W. Chinn, L. Kelly, H. Jeong, C.C. Huang, D. Stryke, M. Kawamoto, S.J. Johns, E. Carlson, T. Taylor, T.E. Ferrin, A. Sali, K.M. Giacomini, D.L. Kroetz. "PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network." Pharmacol Rev 58, 1-2, 2006.

169. H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, R.L. Dunbrack Jr., K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley, J. Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost, H. Saibil, T. Schwede, D.M. Standley, J.D. Westbrook. "Outcome of a workshop on archiving structural models of biological macromolecules." Structure 14, 1211-1217, 2006.

170. A. Colubri, A.K. Jha, M.Y. Shen, A. Sali, R.S. Berry, T.R. Sosnick, K.F. Freed. "Minimalist representations and the importance of nearest neighbor effects in protein folding simulations." J Mol Biol 363, 835-857, 2006.

171. M.Y. Shen, A. Sali. "Statistical potential for assessment and prediction of protein structures." Protein Sci 15, 2507-2524, 2006.

172. N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper, A. Sali. "Comparative protein structure modeling using MODELLER." Curr Protoc Bioinformatics Chapter 5, Unit 5.6.1-5.6.30, 2006.

173. R. Karchin, A.N. Monteiro, S.V. Tavtigian, M.A. Carvalho, A. Sali. "Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning." PLoS Computational Biology 3, e26, 2007.

174. L. Kelly, R. Karchin, A. Sali. "Protein interactions and disease phenotypes in the ABC transporter superfamily." Pac Symp Biocomput, 51-63, 2007.

175. N. Eswar, A. Sali. "Comparative Modeling of Drug Target Proteins." In: Volume 4 Computer-Assisted Drug Design, Comprehensive Medicinal Chemistry II. Ed: J. Taylor, D. Triggle, J.S. Mason, pp. 215-236, Elsevier Ltd, Oxford, UK, 2007.

176. M.A. Carvalho, S.M. Marsillac, R. Karchin, S. Manoukian, S. Grist, R.F. Swaby, T.P. Urmenyi, E. Rondinelli, R. Silva, L. Gayol, L. Baumbach, R. Sutphen, J.L. Pickard-Brzosowicz, K.L. Nathanson, A. Sali, D. Goldgar, F.J. Couch, P. Radice, A.N. Monteiro. "Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis." Cancer Res 67, 1494-1501, 2007.

177. S.X. Wang, K.C. Pandey, J. Scharfstein, J. Whisstock, R.K. Huang, J. Jacobelli, R.J. Fletterick, P.J. Rosenthal, M. Abrahamson, L.S. Brinen, A. Rossi, A. Sali, J.H. McKerrow. "The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family." Structure 15, 535-543, 2007.


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178. E. Feyfant, A. Sali, A. Fiser. "Modeling mutations in protein structures." Protein Sci 16, 2030-2041, 2007.

179. N. Soranzo, L. Kelly, L. Martinian, M.W. Burley, M. Thom, A. Sali, D.L. Kroetz, D.B. Goldstein, S.M. Sisodiya. "Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy." Epilepsia 48, 674-683, 2007.

180. K. Bajaj, M.S. Madhusudhan, B.V. Adkar, P. Chakrabarti, C. Ramakrishnan, A. Sali, R. Varadarajan. "Stereochemical criteria for prediction of the effects of proline mutations on protein stability." PLoS Comput Biol 3, e241, 2007.

181. R. Aragues, A. Sali, J. Bonet, M.A. Marti-Renom, B. Oliva. "Characterization of protein hubs by inferring interacting motifs from protein interactions." PLoS Comput Biol 3, 1761-1771, 2007.

182. M.A. Marti-Renom, A. Rossi, F. Al-Shahrour, F.P. Davis, U. Pieper, J. Dopazo, A. Sali. "The AnnoLite and AnnoLyze programs for comparative annotation of protein structures." BMC Bioinformatics 8 Suppl 4, S4, 2007.

183. M.A. Marti-Renom, U. Pieper, M.S. Madhusudhan, A. Rossi, N. Eswar, F.P. Davis, F. Al-Shahrour, J. Dopazo, A. Sali. "DBAli tools: mining the protein structure space." Nucleic Acids Res 35, W393-397, 2007.

184. F.P. Davis, D.T. Barkan, N. Eswar, J.H. McKerrow, A. Sali. "Host pathogen protein interactions predicted by comparative modeling." Protein Sci 16, 2585-2596, 2007.

185. S.C. Almo, J.B. Bonanno, J.M. Sauder, S. Emtage, T.P. Dilorenzo, V. Malashkevich, S.R. Wasserman, S. Swaminathan, S. Eswaramoorthy, R. Agarwal, D. Kumaran, M. Madegowda, S. Ragumani, Y. Patskovsky, J. Alvarado, U.A. Ramagopal, J. Faber-Barata, M.R. Chance, A. Sali, A. Fiser, Z.Y. Zhang, D.S. Lawrence, S.K. Burley. "Structural genomics of protein phosphatases." J Struct Funct Genom 8, 121-140, 2007.

186. F. Melo, A. Sali. "Fold assessment for comparative protein structure modeling." Protein Sci 16, 2412-2426, 2007.

187. A. Sali, C.D. Lima, M. Kostic. "Structural genomics." Structure 15, 1341, 2007.

188. V.D. Winn, R. Haimov-Kochman, A.C. Paquet, Y.J. Yang, M.S. Madhusudhan, M. Gormley, K.T. Feng, D.A. Bernlohr, S. McDonagh, L. Pereira, A. Sali, S.J. Fisher. "Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term." Endocrinology 148, 1059-1079, 2007.

189. C.V. Robinson, A. Sali, W. Baumeister. "The molecular sociology of the cell." Nature 450, 973-982, 2007.

190. F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B.T. Chait, A. Sali, M.P. Rout. "The molecular architecture of the nuclear pore complex." Nature 450, 695-701, 2007.

191. F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B.T. Chait, M.P. Rout, A. Sali. "Determining the architectures of macromolecular assemblies." Nature 450, 683-694, 2007.

192. N. Eswar, D. Eramian, B. Webb, M.Y. Shen, A. Sali. "Protein structure modeling with MODELLER." Methods Mol Biol 426, 145-159, 2008.


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193. T. Schwede, A. Sali, N. Eswar, M.C. Peitsch. "Protein Structure Modeling." In: Computational Structural Biology. Ed: T. Schwede, M.C. Peitsch, pp. 3-35, World Scientific Publishing Ltd., Singapore, 2008.

194. Y. Cong, M. Topf, A. Sali, P. Matsudaira, M. Dougherty, W. Chiu, M.F. Schmid. "Crystallographic conformers of actin in a biologically active bundle of filaments." J Mol Biol 375, 331-336, 2008.

195. C.R. Booth, A.S. Meyer, Y. Cong, M. Topf, A. Sali, S.J. Ludtke, W. Chiu, J. Frydman. "Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT." Nat Struct Mol Biol 15, 746-753, 2008.

196. S.K. Burley, S.C. Almo, J.B. Bonanno, M.R. Chance, S. Emtage, A. Fiser, A. Sali, J.M. Sauder, S. Swaminathan. "Structure Genomics of Protein Superfamilies." In: Structural Bioinformatics, 2nd Edition. Ed: J. Gu, P.E. Bourne, Wiley-Blackwell, New York, NY, 2008.

197. F. Alber, B.T. Chait, M.P. Rout, A. Sali. "Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints." In: Protein-protein interactions and networks: identification, characterization and prediction. Ed: A. Panchenko, T. Przytycka, pp. 99-114, Springer-Verlag, London, UK, 2008.

198. P. Chandramouli, M. Topf, J.F. Menetret, N. Eswar, J.J. Cannone, R.R. Gutell, A. Sali, C.W. Akey. "Structure of the mammalian 80S ribosome at 8.7 A resolution." Structure 16, 535-548, 2008.

199. F. Alber, F. Forster, D. Korkin, M. Topf, A. Sali. "Integrating diverse data for structure determination of macromolecular assemblies." Annu Rev Biochem 77, 443-477, 2008.

200. M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, A. Sali. "Protein structure fitting and refinement guided by cryo-EM density." Structure 16, 295-307, 2008.

201. J. Espadaler, N. Eswar, E. Querol, F.X. Aviles, A. Sali, M.A. Marti-Renom, B. Oliva. "Prediction of enzyme function by combining sequence similarity and protein interactions." BMC Bioinformatics 9, 249, 2008.

202. F. Aguero, B. Al-Lazikani, M. Aslett, M. Berriman, F.S. Buckner, R.K. Campbell, S. Carmona, I.M. Carruthers, A.W. Chan, F. Chen, G.J. Crowther, M.A. Doyle, C. Hertz-Fowler, A.L. Hopkins, G. McAllister, S. Nwaka, J.P. Overington, A. Pain, G.V. Paolini, U. Pieper, S.A. Ralph, A. Riechers, D.S. Roos, A. Sali, D. Shanmugam, T. Suzuki, W.C. Van Voorhis, C.L. Verlinde. "Genomic-scale prioritization of drug targets: the TDR Targets database." Nat Rev Drug Discov 7, 900-907, 2008.

203. R. Karchin, M. Agarwal, A. Sali, F. Couch, M.S. Beattie. "Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios." Cancer Inform 6, 203-216, 2008.

204. K.A. Krukenberg, F. Forster, L.M. Rice, A. Sali, D.A. Agard. "Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90." Structure 16, 755-765, 2008.

205. D. Eramian, N. Eswar, M.Y. Shen, A. Sali. "How well can the accuracy of comparative protein structure models be predicted?" Protein Sci 17, 1881-1893, 2008.

206. F. Forster, B. Webb, K.A. Krukenberg, H. Tsuruta, D.A. Agard, A. Sali. "Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies." J Mol Biol 382, 1089-1106, 2008.


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207. C.M. Anderson, D. Korkin, D.L. Smith, S. Makovets, J.J. Seidel, A. Sali, E.H. Blackburn. "Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break." Genes Dev 22, 854-859, 2008.

208. R.A. Chiang, A. Sali, P.C. Babbitt. "Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies." PLoS Comput Biol 4, e1000142, 2008.

209. S. Mahrus, J.C. Trinidad, D.T. Barkan, A. Sali, A.L. Burlingame, J.A. Wells. "Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini." Cell 134, 866-876, 2008.

210. I.I. Serysheva, S.J. Ludtke, M.L. Baker, Y. Cong, M. Topf, D. Eramian, A. Sali, S.L. Hamilton, W. Chiu. "Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel." Proc Natl Acad Sci U S A 105, 9610-9615, 2008.

211. S. Graslund, P. Nordlund, J. Weigelt, B.M. Hallberg, J. Bray, O. Gileadi, S. Knapp, U. Oppermann, C. Arrowsmith, R. Hui, J. Ming, S. dhe-Paganon, H. Park, A. Savchenko, A. Yee, A. Edwards, R. Vincentelli, C. Cambillau, R. Kim, S. Kim, Z. Rao, Y. Shi, T.C. Terwilliger, C. Kim, L. Hung, G.S. Waldo, Y. Peleg, S. Albeck, T. Unger, O. Dym, J. Prilusky, J.L. Sussman, R.C. Stevens, S.A. Lesley, I.A. Wilson, A. Joachimiak, F. Collart, I. Dementieva, M.I. Donnelly, W.H. Eschenfeldt, Y. Kim, L. Stols, R. Wu, M. Zhou, S.K. Burley, J.S. Emtage, J.M. Sauder, D. Thompson, K. Bain, J. Luz, T. Gheyi, F. Zhang, S. Atwell, S.C. Almo, J.B. Bonanno, A. Fiser, S. Swaminathan, F.W. Studier, M.R. Chance, A. Sali, T.B. Acton, R. Xiao, L. Zhao, L.C. Ma, J.F. Hunt, L. Tong, K. Cunningham, M. Inouye, S. Anderson, H. Janjua, R. Shastry, C.K. Ho, D. Wang, H. Wang, M. Jiang, G.T. Montelione, D.I. Stuart, R.J. Owens, S. Daenke, A. Schutz, U. Heinemann, S. Yokoyama, K. Bussow, K.C. Gunsalus. "Protein production and purification (vol 5, pg 135, 2008)." Nat Methods 5, 369-369, 2008.

212. N. Eswar, A. Sali. "Protein Structure Modeling." In: From Molecules to Medicine, Structure of Biological Macromolecules and Its Relevance in Combating New Diseases and Bioterrorism. Ed: J.L. Sussman, P. Spadon, pp. 139-151, Springer-Verlag, Dordrecht, The Netherlands, 2009.

213. U. Pieper, R. Chiang, J.J. Seffernick, S.D. Brown, M.E. Glasner, L. Kelly, N. Eswar, J.M. Sauder, J.B. Bonanno, S. Swaminathan, S.K. Burley, X. Zheng, M.R. Chance, S.C. Almo, J.A. Gerlt, F.M. Raushel, M.P. Jacobson, P.C. Babbitt, A. Sali. "Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies." J Struct Funct Genom 10, 107-125, 2009.

214. U. Pieper, N. Eswar, B.M. Webb, D. Eramian, L. Kelly, D.T. Barkan, H. Carter, P. Mankoo, R. Karchin, M.A. Marti-Renom, F.P. Davis, A. Sali. "MODBASE, a database of annotated comparative protein structure models and associated resources." Nucleic Acids Res 37, D347-354, 2009.

215. F.A. Hays, Z. Roe-Zurz, M. Li, L. Kelly, F. Gruswitz, A. Sali, R.M. Stroud. "Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination." J Struct Funct Genom 10, 9-16, 2009.

216. M. Li, F.A. Hays, Z. Roe-Zurz, L. Vuong, L. Kelly, C.M. Ho, R.M. Robbins, U. Pieper, J.D. O'Connell 3rd, L.J. Miercke, K.M. Giacomini, A. Sali, R.M. Stroud. "Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening." J Mol Biol 385, 820-830, 2009.


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217. M.E. Peterson, F. Chen, J.G. Saven, D.S. Roos, P.C. Babbitt, A. Sali. "Evolutionary constraints on structural similarity in orthologs and paralogs." Protein Sci 18, 1306-1315, 2009.

218. D. Russel, K. Lasker, J. Phillips, D. Schneidman-Duhovny, J.A. Velazquez-Muriel, A. Sali. "The structural dynamics of macromolecular processes." Curr Opin Cell Biol 21, 97-108, 2009.

219. T. Schwede, A. Sali, B. Honig, M. Levitt, H.M. Berman, D. Jones, S.E. Brenner, S.K. Burley, R. Das, N.V. Dokholyan, R.L. Dunbrack Jr, K. Fidelis, A. Fiser, A. Godzik, Y.J. Huang, C. Humblet, M.P. Jacobson, A. Joachimiak, S.R. Krystek Jr, T. Kortemme, A. Kryshtafovych, G.T. Montelione, J. Moult, D. Murray, R. Sanchez, T.R. Sosnick, D.M. Standley, T. Stouch, S. Vajda, M. Vasquez, J.D. Westbrook, I.A. Wilson. "Outcome of a workshop on applications of protein models in biomedical research." Structure 17, 151-159, 2009.

220. L. Orti, R.J. Carbajo, U. Pieper, N. Eswar, S.M. Maurer, A.K. Rai, G. Taylor, M.H. Todd, A. Pineda-Lucena, A. Sali, M.A. Marti-Renom. "A kernel for open source drug discovery in tropical diseases." PLoS Negl Trop Dis 3, e418, 2009.

221. K.C. Pandey, D.T. Barkan, A. Sali, P.J. Rosenthal. "Regulatory elements within the prodomain of falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum." PLoS One 4(5):e5694, 2009.

222. R.M. Stroud, S. Choe, J. Holton, H.R. Kaback, W. Kwiatkowski, D.L. Minor, R. Riek, A. Sali, H. Stahlberg, W. Harries. "2007 Annual progress report synopsis of the Center for Structures of Membrane Proteins." J Struct Funct Genom 10, 193-208, 2009.

223. L. Orti, R.J. Carbajo, U. Pieper, N. Eswar, S.M. Maurer, A.K. Rai, G. Taylor, M.H. Todd, A. Pineda-Lucena, A. Sali, M.A. Marti-Renom. "A kernel for the Tropical Disease Initiative." Nat Biotechnol 27, 320-321, 2009.

224. O. Fornes, R. Aragues, J. Espadaler, M.A. Marti-Renom, A. Sali, B. Oliva. "ModLink+: Improving fold recognition by using protein-protein interactions." Bioinformatics 25, 1506-1512, 2009.

225. S. Nickell, F. Beck, S.H.W. Scheres, A. Korinek, F. Forster, K. Lasker, O. Mihalache, N. Sun, I. Nagy, A. Sali, J. Plitzko, J.-M. Carazo, M. Mann, W. Baumeister. "Insights into the Molecular Architecture of the 26S Proteasome." Proc Natl Acad Sci U S A 29, 11943-11947, 2009.

226. K. Lasker, M. Topf, A. Sali, H.J. Wolfson. "Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly." J Mol Biol 388, 180-194, 2009.

227. M.S. Madhusudhan, B.M. Webb, M.A. Marti-Renom, N. Eswar, A. Sali. "Alignment of multiple protein structures based on sequence and structure features." Protein Eng Des Sel 22, 569-574, 2009.

228. J.A. DeGrasse, K.N. DuBois, D. Devos, T.N. Siegel, A. Sali, M.C. Field, M.P. Rout, B.T. Chait. "The Establishment of Nuclear Pore Complex Architecture Occurred Early in Evolution." Mol Cell Proteomics 8, 2119-2130, 2009.

229. L. Kelly, U. Pieper, N. Eswar, F.A. Hays, M. Li, Z. Roe-Zurz, D. Kroetz, K.M. Giacomini, R.M. Stroud, A. Sali. "A survey of integral alpha-helical membrane proteins." J Struct Funct Genomics 10, 269-280, 2009.


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230. T. Lezon, A. Sali, I. Bahar. "Global motions of the nuclear pore complex:Insights from Elastic Network Models." PLoS Comp Biol 5, e1000496, 2009.

231. D.J. Taylor, B. Devkota, A.D. Huang, M. Topf, N. Eswar, A. Sali, S.C. Harvey, J. Frank. "Comprehensive Molecular Structure of the Eukaryotic Ribosome." Structure 17, 1591-1604, 2009.

232. H. Fan, J.J. Irwin, B.M. Webb, G. Klebe, B. Shoichet, A. Sali. "Molecular Docking Screens Using Comparative Models of Proteins." J Chem Inf Model 49, 2512-2527, 2009.

233. F. Forster, K. Lasker, F. Beck, S. Nickell, A. Sali, W. Baumeister. "An Atomic Model AAA-ATPase/20S core particle sub-complex of the 26S proteasome." Biochem Biophys Res Commun 388, 228-233, 2009.

234. D. Kroetz, N. Ahituv, E. Burchard, S. Guo, A. Sali, K. Giacomini. "The Pharmacogenomics Center of the University of California, Sam Francisco: At the interface of genomics, biological mechanism and drug therapy." Pharmacogenomics 10, 1569-1576, 2009.

235. F.P. Davis, A. Sali. "The overlap of small molecule and protein binding sites within families of protein structures." PLoS Comp Biol 6, e1000668, 2010.

236. D. Barkan, D. Hostetter, S. Mahrus, U. Pieper, J. Wells, C. Craik, A. Sali. "Prediction of Protease Substrates using Sequence and Structure Features." Bioinformatics 26, 1714-1722, 2010.

237. F. Gruswitz, S. Chaudhary, J. Ho, A. Schlessinger, P. Bobak, C. Ho, A. Sali, C. Westhoff, R. Stroud. "Function of Human Rh based on Structure of RhCG at 2.1 Å." Proc Natl Acad Sci U S A 107, 9638-9643, 2010.

238. L. Chen, B. Pawlikowski, A. Schlessinger, S. More, D. Stryke, S.J. Johns, M. Portman, T.E. Ferrin, A. Sali, K. Giacomini. "Role of organic cation transporter 3 (SLC22A3) and Its missense variants in the pharmacologic action of metformin." Pharmacogenet Genomics 20, 687-699, 2010.

239. A. Schlessinger, P. Matsson, J.E. Shima, U. Pieper, S.W. Yee, L. Kelly, L. Apeltsin, R.M. Stroud, T.E. Ferrin, K.M. Giacomini, A. Sali. "Comparison of Human Solute Carriers." Protein Sci 19, 412-428, 2010.

240. D. Schneidman-Duhovny, M. Hammel, A. Sali. "FoXS: A Web Server for Rapid Computation and Fitting of SAXS Profiles." Nucleic Acids Res 38, 541-544, 2010.

241. K. Lasker, J.L. Phillips, D. Russel, J. Velazquez-Muriel, D. Schneidman-Duhovny, B. Webb, A. Schlessinger, A. Sali. "Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data." Mol Cell Proteomics 9, 1689-1702, 2010.

242. P. Sampathkumar, S.A. Ozyurt, J. Do, K.T. Bain, M. Dickey, L.A. Rodgers, T. Gheyi, A. Sali, S.J. Kim, J. Phillips, U. Pieper, J. Fernandez-Martinez, J.D. Franke, A. Martel, H. Tsuruta, S. Atwell, D.A. Thompson, J.S. Emtage, S.R. Wasserman, M.P. Rout, J.M. Sauder, S.K. Burley. "Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup 145." Proteins:Struct Funct Bioinform 78, 1992-1998, 2010.

243. P. Sampathkumar, F. Lu, X. Zhao, Z. Li, J. Gilmore, K. Bain, M.E. Rutter, T. Gheyi, K. Schwinn, J. Bonanno, U. Pieper, J.E. Fajardo, A. Fiser, S. Almo, A. Swaminathan, M. Chance, D. Baker, S. Atwell, D. Thompson, J.S. Emtage, S. Wasserman, A. Sali, J.M.


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Sauder, S. Burley. "Structure of a putative BenF-like porin from Pseudomanas fluorescens Pf-5 at 2.6 Å resolution." Proteins:Struct Funct Bioinform 78, 3056-3062, 2010.

244. K. Lasker, A. Sali, H.J. Wolfson. "Determining macromolecular assembly structures by molecular docking and fitting into an electron density map." Proteins:Struct Funct Bioinform 78, 3205-3211, 2010.

245. L. Chen, M. Takizawa, E. Chen, A. Schlessinger, J.H. Choi, J. Segenthelar, A. Sali, M. Kubo, S. Nakamura, Y. Iwamoto, N. Iwasaki, K.M. Giacomini. "Genetic polymorphisms in the organic cation transporter 1, OCT1, in Chinese and Japanese populations, exhibit altered function." J Pharmacol Exp Ther 1, 42-50, 2010.

246. L. Kelly, H. Fukushima, R. Karchin, J.M. Gow, L.W. Chinn, U. Pieper, M.R. Segal, D.L. Kroetz, A. Sali. "Functional Hot Spots in Human ATP-binding Cassette Transporter Nucleotide Binding Domains." Protein Sci 19, 2110-2121, 2010.

247. F. Forster, K. Lasker, S. Nickell, A. Sali, W. Baumeister. "Toward an integrated structural model of the 26S proteasome." Mol Cell Proteomics 9, 1666-1677, 2010.

248. D. Schneidman-Duhovny, M. Hammel, A. Sali. "Macromolecular docking restrained by a small angle X-ray scattering profile." J Struct Biol 3, 461-471, 2011.

249. L. Kelly, H. Fukushima, R. Karchin, J.M. Gow, L.W. Chinn, U. Pieper, M.R. Segal, D.L. Kroetz, A. Sali. "Response to "Predictable difficulty or difficulty to predict" by Tamas Aranyi, Krisztina Fulop, Orsolya Symmons, Viola Pomozi, and Andras Varadi." Protein Sci 20, 4-5, 2011.

250. U. Pieper, B.M. Webb, D.T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, H. Braberg, Z. Yang, E.C. Meng, E.F. Pettersen, C.C. Huang, R.S. Datta, P. Sampathkumar, M.S. Madhusudhan, K. Sjolander, T.E. Ferrin, S.K. Burley, A. Sali. "ModBase, a database of annotated comparative protein structure models, and associated resources." Nucleic Acids Res 39, 465-474, 2011.

251. S.S. Kamat, A. Bagaria, D. Kumaran, G.P. Holmes-Hampton, H. Fan, A. Sali, J.M. Sauder, S.K. Burley, P.A. Lindahl, S. Swaminathan, F.M. Raushel. "Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase." Biochemistry (Mosc) 50, 1917-1927, 2011.

252. B. Webb, K. Lasker, D. Schneidman-Duhovny, E. Tjioe, J. Phillips, S.J. Kim, J. Velazquez-Muriel, D. Russel, A. Sali. "Modeling of Proteins and their Assemblies with the Integrative Modeling Platform." In: Methods in Molecular Biology, pp. 377-397, Humana Press, 2011.

253. P. Sampathkumar, T. Gheyi, S.A. Miller, K.T. Bain, M. Dickey, J.B. Bonanno, Kim. S.J., J. Phillips, U. Pieper, J. Fernandez-Martinez, J. Franke, A. Martel, H. Tsuruta, S. Atwell, D.A. Thompson, J.S. Emtage, S.R. Wasserman, M.P. Rout, A. Sali, J.M. Sauder, S.K. Burley. "Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the Nuclear Pore Complex." Proteins:Struct Funct Bioinform 79, 1672-1677, 2011.

254. S.S. Kamat, H. Fan, J.M. Sauder, S.K. Burley, B.K. Shoichet, A. Sali, F.M. Raushel. "Enzymatic deamination of the epigenetic base N-6-methyladenine." J Am Chem Soc 133, 2080-2083, 2011.

255. S. Dokudovskaya, F. Waharte, A. Schlessinger, U. Pieper, D.P. Devos, I.M. Cristea, R. Williams, J. Salamero, B.T. Chait, A. Sali, M.C. Field, M.C. Rout, C. Dargemont. "A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae." Mol Cell Proteomics, M110.006478, 2011.


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256. M. Field, A. Sali, M. Rout. "On a bender: Bars, ESCRTs, COPs, and finally getting your coat." J Cell Biol 193, 963-972, 2011.

257. H. Fan, D. Schneidman, J.J. Irwin, G. Dong, B. Shoichet, A. Sali. "Statistical Potential for Modeling and Ranking Protein-Ligand Interactions." J Chem Inf Model 51, 3078-3092, 2011.

258. S. Jager, P. Cimermancic, N. Gulbahce, J. Johnson, K. McGovern, S. Clarke, M. Shales, G. Mercenne, K. Li, H. Barry, G. Jang, E. Akiva, L. Pache, J. Marlett, S. Roth, M. Stephens, I. D'Orso, J. Fernandes, M. Fahey, C. Mahon, A. O'Donoghue, A. Todorovic, J. Morris, D. Maltby, T. Alber, G. Cagney, F. Bushman, J. Young, S. Chanda, W. Sundquist, T. Kortemme, R. Hernandez, C. Craik, A. Burlingame, A. Sali, A. Frankel, N. Krogan. "Global Landscape of HIV-Human Protein Complexes." Nature 481, 365-370, 2011.

259. S. Jager, D.Y. Kim, K. Shindo, E. Kwon, R. LaRue, C. Mahon, P. Cimermancic, L. Yen, D. Stanley, M. Li, A. Burlingame, A. Sali, C. Craik, R. Harris, J. Gross, N. Krogan. "Vif Hijacks CBFÎ² to Degrade APOBEC3G and Promote HIV-1 Infection." Nature 481, 371-375, 2011

260. E. Tjioe, K. Lasker, B. Webb, H. Wolfson, A. Sali. "MultiFit: A web server for fitting multiple protein structures into their electron microscopy density map." Nucleic Acids Res 39, 167-170, 2011.

261. J. Carlsson, R. Coleman, V. Setola, J. Irwin, H. Fan, A. Schlessinger, A. Sali, B. Roth, B. Shoichet. "Structure-based Ligand Discovery Against a Homology Model and X-ray Structure of the Dopamine D3 Receptor." Nat Chem Biol 7, 769-778, 2011.

262. A. Schlessinger, E. Geier, H. Fan, J. Irwin, B. Shoichet, K. Giacomini, A. Sali. "Structure-based Discovery of Prescription Drugs that Interact with the Norepinephrine Transporter, NET." Proc Natl Acad Sci USA 108, 15810-15815, 2011.

263. 263. J. Choi, S. Yee, A. Ramirez, K. Morrissey, G. Jang, P. Joski, J. Mefford, S. Hesselson, A. Schlessinger, G. Jenkins, R. Castro, S. Johns, D. Stryke, A. Sali, T. Ferrin, J. Witte, P. Kwok, D. Roden, R. Wilke, C. McCarty, R. Davis, K. Giacomini. "A Common Promoter Variant in MATE2-K Is Associated with Poor Response to Metformin." Clin Pharmacol Ther 90, 674-684, 2011.

264. Z. Yang, K. Lasker, D. Schneidman-Duhovny, B. Webb, C. Huang, E. Pettersen, T. Goddard, E. Meng, A. Sali, T. Ferrin. "UCSF Chimera, MODELLER, and IMP: an integrated Modeling System." J Struct Biol 179, 269-278, 2011.

265. 265. A.M. Goble, H. Fan, A. Sali, F.M. Raushel. "Discovery of a Cytokinin Deaminase." ACS Chem Biol 6, 1036-1040, 2011.

266. J. Gerlt, K. Allen, S. Almo, R. Armstrong, P. Babbitt, J. Cronan, D. Dunaway-Mariano, H. Imker, M. Jacobson, W. Minor, C. Poulter, F. Raushel, A. Sali, B. Shoichet, J. Sweedler. "The Enzyme Function Initiative." Biochemistry 50, 9950-9962, 2011

267. K. Lasker, J. Velazquez-Muriel, B. Webb, Z. Yang, T.E. Ferrin, A. Sali. "Macromolecular assembly structures by comparative modeling and electron microscopy." In: Methods in Molecular Biology. Ed: J. Walker, Humana Press, New York, NY, 2011.

268. H. Fan, J. Irwin, A. Sali. "Virtual Ligand Screening Against Comparative Protein Structure Models." Methods Mol Biol 819, 105-126, 2012.


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269. J. Fernandez-Martinez, J. Phillips, M. Sekedat, R. Diaz-Avalos, J. Velazquez-Muriel, J. Franke, R. Williams, D. Stokes, B. Chait, A. Sali, M. Rout. "Structure-function Map for a Heptameric Component of the Nuclear Pore Complex." J Cell Biol 196, 419-434, 2012.

270. R. Henderson, A. Sali, H. Berman, W. Chiu, G. Kleyweft, C. Lawson, M. Baker, B. Carragher, B. Devkota, K. Downing, E. Egelman, Z. Feng, J. Frank, N. Grigorieff, W. Jiang, S. Ludtke, O. Medalia, P. Penczek, P. Rosenthal, M. Rossmann, M. Schmid, G. Schroder, A. Steven, D. Stokes, J. Westbrook, W. Wriggers, H. Yang, J. Young. "Outcome of the First Electron Microscopy Validation Task Force Meeting." Structure 20, 205-214, 2012.

271. P. Weinkam, J. Pons, A. Sali. "Structure-based Model of Allostery Predicts Coupling Between Distant Sites." Proc Natl Acad Sci USA 109, 4875-4880, 2012.

272. D. Russel, K. Lasker, B. Webb, J. Velazquez-Muriel, E. Tjioe, D. Schneidman-Duhovny, B. Peterson, A. Sali. "Putting the pieces together: integrative structure determination of macromolecular assemblies." PLoS Biol 10, e1001244, 2012.

273. G. Pathare, I. Nagy, S. Bohn, P. Unverdorben, A. Hubert, R. Korner, S. Nickell, K. Lasker, A. Sali, T. Tamura, T. Nishioka, F. Forster, W. Baumeister, A. Bracher. "The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together." Proc Natl Acad Sci USA 109, 149-154, 2012.

274. K. Lasker, F. Forster, S. Bohn, T. Walzthoeni, E. Villa, P. Unverdorben, F. Beck, R. Aebersold, A. Sali, W. Baumeister. "Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach." Proc Natl Acad Sci USA 109, 1380-1387, 2012.

275. P. Sampathkumar, S.J. Kim, D. Manglicmot, K.T. Bain, J. Gilmore, T. Gheyi, J. Phillips, U. Pieper, J. Fernandez-Martinez, J. Franke, T. Matsui, H. Tsuruta, S. Atwell, D. Thompson, J.S. Emtage, S. Wasserman, M. Rout, A. Sali, J.M. Sauder, S.C. Almo, S.K. Burley. "Atomic structure of the Nuclear Pore Complex targeting domain of Nup116 homologue from the yeast, Candida glabrata." Proteins:Struct Funct Bioinform 8, 2110-2116, 2012.

276. C. Klammt, I. Maslennikov, M. Bayrhuber, C. Eichmann, N. Vajpai, E. Chiu, K. Blain, L. Esquivies, H. Kwon, B. Balana, U. Pieper, A. Sali, P. Slesinger, W. Kwiatkowski, R. Rick, S. Choe. "Facile Backbone structure determination of human membrane proteins by NMR spectroscopy." Nat Methods 8, 834-839, 2012.

277. D. Schneidman-Duhovny, A. Rossi, A. Avila-Sakar, S.J. Kim, J. Velazquez-Muriel, P. Strop, H. Liang, K.A. Krukenberg, M. Liao, H.M. Kim, S. Sobhanifar, V. Dotsch, A. Raipal, J. Pons, D.A. Agard, Y. Cheng, A. Sali. "A Method for Integrative Structure Determination of Protein-Protein Complexes." Bioinformatics 28, 3282-3289, 2012.

278. V. Puizdar, T. Zajc, E. Zerovnik, M. Renko, U. Pieper, N. Eswar, A. Sali, I. Dolenc, V. Turk. "Biochemical Characterization and Structural Modeling of Human Cathepsin E Variant 2 in Comparison to the Wild-type Protein." Biol Chem 393, 177-186, 2012.

279. A. Morin, J. Urban, P.D. Adams, I. Foster, A. Sali, D. Baker, P. Sliz. "Shining Light into Black Boxes." Science 336, 159-160, 2012.

280. H. Braberg, B. Webb, E. Tjioe, U. Pieper, A. Sali, M.S. Madhusudhan. "SALIGN: A webserver for alignment of multiple protein sequences and structures." Bioinformatics 15, 2072-2073, 2012.


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281. J.A. Horst, U. Pieper, A. Sali, L. Zhan, G. Chopra, R. Samudrala, J.D.B. Featherstone. "Strategic protein target analysis for developing drugs to stop dental caries." Adv Dent Res 22, 86-93, 2012.

282. J. Trinidad, D. Barkan, B. Gulledge, A. Thalhammer, A. Sali, R. Schoepfer, A. Burlingame. "Global Identification and Characterization of Both O-GlcNAcylation and Phosphorylation at the Murine Synapse." Mol Cell Proteomics 11, 215-229, 2012.

283. O. Martinez-Avila, S. Wu, S.J. Kim, Y. Cheng, F. Khan, R. Samudrala, A. Sali, J. Horst, S. Habelitz. "Self-assembly of Filamentous Amelogenin Requires Calcium and Phosphate: From Dimers via Nanoribbons to Fibrils." Biomacromolecules 13, 3494-3502, 2012.

284. J.A. Velazquez-Muriel, K. Lasker, D. Russel, J. Phillips, B. Webb, D. Schneidman-Duhovny, A. Sali. "Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images." Proc Natl Acad Sci USA 109, 18821-18826, 2012.

285. P. Kolb, K. Phan, Z. Gao, A. Marko, A. Sali, K.A. Jacobson. "Limits of ligand selectivity from docking to models: In silico screening for A1 adenosine receptor antagonists." PLoS One 7, e49910, 2012.

286. A. Schlessinger, M.B. Wittwer, A. Dahlin, N. Khuri, M. Bonomi, H. Fan, K. Giacomini, A. Sali. "High Selectivity of the Î³-Aminobutyric Acid Transporter 2 (GAT-2, SLC6A13) Revealed by Structure-based Approach." J Biol Chem 287, 37745-37756, 2012.

287. D. Schneidman-Duhovny, S.J. Kim, A. Sali. "Integrative structural modeling with small angle X-ray scattering profiles." BMC Struct Biol 12, 17, 2012.

288. Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski M, Case D, Chazin W, Cross T, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay L, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil R, HO C, Rule G, Gronenborn A, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue E, Mott H, Nietlispach D, Barsukiv I, Lian L, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis I, Watts A, Conte M, Mason J, Pfuhl M, Sanderson M, Craven J, Williamson M, Dominguez C, Roberts G, Gunther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw D, Steinbeck C, Vendruscolo M, Vuister G, Walters K, Weinstein H, Wuthrich K, Yodoyama S. In support of the BMRB. Nat Struct Mol Biol 19, 854-860, 2012. PMCID TBD by Journal

289. H. Fan, D. Hitchcock, R. Seidel, B. Hillerich, H. Lin, S. Almo, A. Sali, B. Shoichet, F. Raushel. "The Assignment of Pterin Deaminase Activity to an Enzyme of Unknown Function Guided by Homology Modeling and Docking." J Am Chem Soc 135, 795-803, 2013.

290. M.B. Wittwer, A.A. Zur, N. Khuri, Y. Kido, A. Kosaka, X. Zhang, K.M. Morrissey, A. Sali, Y. Huang, K.M. Giacomini. "Discovery of potent, selective multidrug and toxin extrusion Transporter 1 (MATE1, SLC47A1) inhibitors through prescription drug profiling and computational modeling." J Med Chem 56, 781-795, 2013.

291. U. Pieper, A. Schlessinger, E. Kloppmann, G.A. Chang, J.J. Chou, M. Dumont, B. Fox, P. Fromme, W. Hendrickson, M. Malkowski, D. Rees, D. Stokes, M.H.B. Stowell, M. Wiener,


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B. Rost, R. Stroud, R. Stevens, A. Sali. "Coordinating the impact of structural genomics on the human a-helical transmembrane proteome." Nat Struct Mol Biol 20, 135-138, 2013.

292. P. Sampathkumar, S.J. Kim, P. Upla, W. Rice, J. Phillips, B. Timney, U. Pieper, J. Bonanno, J. Fernandez-Martinez, Z. Hakhverdyan, N. Ketaren, T. Matsui, R. Weiss, D. Stokes, J.M. Sauder, S. Burley, A. Sali, M. Rout, S. Almo. "Structure, dynamics, evolution and function of a major scaffold component in the Nuclear Pore Complex." Structure 21, 560-571, 2013.

293. H. Gradisar, S. Bozic, T. Doles, D. Vengust, I. Hafner-Bratkovic, A. Mertelj, B. Webb, A. Sali, S. Klavzar, R. Jerala. "Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments." Nat Chem Biol 9, 362-366, 2013.

294. B. Pedersen, H. Kumar, A. Waight, A. Risenmay, Z. Roe-Zurz, B. Chau, A. Schlessinger, M. Bonomi, W. Harries, A. Sali, A. Johri, R. Stroud. "Crystal structure of a eukaryotic phosphate transporter." Nature 496, 533-536, 2013.

295. A. Schlessinger, N. Khuri, K. Giacomini, A. Sali. "Molecular modeling and ligand docking for Solute Carrier (SLC) transporters." Curr Top Med Chem 13, 843-856, 2013.

296. T. van Dam, M. Townsend, M. Turk, A. Schlessinger, A. Sali, M. Field, M. Huynen. "Evolution of modular intraflagellar transport from a coatomer-like progenitor." Proc Natl Acad Sci USA 110, 6943-6948, 2013.

297. A. Waight, B. Pedersen, A. Schlessinger, M. Bonomi, B. Chau, Z. Roe-Zurz, A. Risenmay, A. Sali, R. Stroud. "Structural basis for alternating access of a Eukaryotic Calcium/Proton exchanger." Nature 499, 107-110, 2013.

298. M. Guttman, P. Weinkam, A. Sali, K. Lee. "All-atom ensemble modeling to analyze small angle X-ray scattering of glycosylated proteins." Structure 21, 321-331, 2013.

299. P. Weinkam, Y.C. Chen, J. Pons, A. Sali. "Impact of mutations on the allosteric conformational equilibrium." J Mol Biol 425, 647-661, 2013.

300. A. Ward, A. Sali, I. Wilson. "Integrative structural biology." Science 339, 913-915, 2013.

301. E. Geier, A. Schlessinger, H. Fan, J. Gable, J. Irwin, A. Sali, K. Giacomini. "Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1." Proc Natl Acad Sci USA 110, 5480-5485, 2013.

302. A. Schlessinger, S.W. Yee, A. Sali, K. Giacomini. "SLC classification: an update." Clin Pharmacol Ther 94, 19-23, 2013.

303. J. Trewhella, W. Hendrickson, G. Kleywegt, A. Sali, M. Sato, T. Schwede, D. Svergun, J. Tainer, J. Westbrook, H. Berman. "Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB." Structure 21, 875-881, 2013

304. D. Schneidman-Duhovny, M. Hammel, J. Tainer, A. Sali. "Accurate SAXS profile computation and its assessment by contrast variation experiments." Biophys J 105, 962-974, 2013.

305. B. Webb, N. Eswar, H. Fan, N. Khuri, U. Pieper, G.Q. Dong, A. Sali. "Comparative Modeling of Drug Target Proteins." In: Chemistry, Molecular Sciences and Chemical Engineering, in press, Elsevier.


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306. D. Hitchcock, H. Fan, J. Kim, M. Vetting, B. Hillerich, R. Seidel, S. Almo, B. Shoichet, A. Sali, F. Raushel. "Structure-guided Discovery of New Deaminase Enzymes." J Am Chem Soc 135, 13927-13933, 2013.

307. C. Pandya, S. Brown, U. Pieper, A. Sali, D. Dunaway-Mariano, P. Babbitt, Y. Xia, K. Allen. "The consequences of domain insertion on sequence-structure divergence in a superfold." Proc Natl Acad Sci USA 110, 3381-3387, 2013.

308. P. Weinkam, A. Sali. "Mapping Polymerization and Allostery of Hemoglobin S Using Point Mutations." J Phys Chem B 117, 13058-13068, 2013.

309. G.Q. Dong, H. Fan, D. Schneidman-Duhovny, B. Webb, A. Sali. "Optimized atomic statistical potentials: Assessment of protein interfaces and loops." Bioinformatics 29, 3158-3166, 2013.

310. F. Martinez-Jimenez, G. Papadatos, L. Yang, I.M. Wallace, V. Kumar, U. Pieper, A. Sali, J.R. Brown, J.P. Overington, M.A. Marti-Renom. "Target prediction for an open access set of compounds active against Mycobacterium tuberculosis." PLoS Comp Biol, epub ahead of print, 2013.

311. M. Kostic, C. Lima, A. Sali. "Celebrating 20 Years of Structural Biology." Structure 21, 1477-1478, 2013.

312. A. Goble, R. Toro, X. Li, A. Ornelas, H. Fan, S. Eswaramoorthy, Y. Patskovsky, B. Hillerich, R. Seidel, A. Sali, B. Shoichet, S. Almo, S. Swaminathan, M. Tanner, F. Raushel. "Deamination of 6-Aminodeoxyfutalosine in Menaquinone Biosynthesis by Distantly Related Enzymes." Biochemistry 52, 6525-6536, 2013.

313. C. Ryan, P. Cimermancic, Z. Szpiechy, A. Sali, R. Hernandez, N. Krogan. "High-resolution network biology: connecting sequence with function." Nat Rev Genet 14, 865-879, 2013.

314. K. Berlin, C.A. Castaneda, D. Schneidman-Duhovny, A. Sali, A. Nava-Tudela, D. Fushman. "Recovering a representative conformational ensemble from underdetermined macromolecular structural data." J Am Chem Soc 135, 16595-16609, 2013.

315. M. Bonomi, E.G. Muller, R. Pellarin, S.J. Kim, D. Russel, R. Ramsden, B.A. Sundin, T.A. Davis, A. Sali. "Determining protein complex structures based on a Bayesian model of in vivo FRET data." Mol Cell Proteomics, epub ahead of print, 2014.

316. U. Pieper, B. Webb, G.Q. Dong, D. Schneidman-Duhovny, H. Fan, S.J. Kim, N. Khuri, Y. Spill, P. Weinkam, M. Hammel, J. Tainer, M. Nilges, A. Sali. "ModBase, a database of annotated comparative protein structure models, and associated resources." Nucleic Acids Res 42, 336-346, 2014.

317. K. Molnar, M. Bonomi, R. Pellarin, G. Clinthorne, G. Gonzalez, S. Goldberg, M. Goulian, A. Sali, W. DeGrado. "Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ." Structure 22, 1239-1251, 2014.

318. B. Webb, K. Lasker, J. Velazquez-Muriel, D. Schneidman-Duhovny, R. Pellarin, M. Bonomi, C. Greenberg, B. Raveh, E. Tjioe, D. Russel, A. Sali. "Modeling of proteins and their assemblies with the Integrative Modeling Platform." In: Structural Genomics. Ed: Y. Chen, pp. 277-295, Humana Press, London, UK, 2014.


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319. Y. Spill, S.J. Kim, D. Schneidman-Duhovny, D. Russel, B. Webb, A. Sali, M. Nilges. "SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes." J Synchrotron Radiat 21, 203-208, 2014.

320. J. Johnson, S. Santos, U. Pieper, A. Sali, N. Krogan, P. Beltrao. "Conservation and structural analysis of the Xenopus laevis phospho-proteome." submitted.

321. G.Q. Dong, S. Calhoun, H. Fan, C. Kalyanaraman, N. London, M. Branch, S. Mashiyama, M. Jacobson, B. Shoichet, P. Babbitt, R. Armstrong, A. Sali. "Prediction of substrates for glutathione transferases by covalent docking." J Chem Inf Model 6, 1687-1699, 2014..

322. R. Algret, J. Fernandez-Martinez, Y. Shi, S.J. Kim, R. Pellarin, P. Cimermancic, E. Cochet, A. Sali, B. Chait, M. Rout, S. Dokudovskaya. "Molecular Architecture and Function of the SEA ComplexÂ - a Modulator of the TORC1 Pathway." Mol Cell Proteomics, epub ahead of print, 2014.

323. T. Street, X. Zeng, R. Pellarin, M. Bonomi, A. Sali, M. Kelly, F. Chu, D. Agard. "Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone." J Mol Biol 12, 2393-2404, 2014.

324. X. Zeng-Elmore, X. Gao, R. Pellarin, D. Schneidman-Duhovny, X. Zhang, K. Kozacka, Y. Tang, A. Sali, R. Chalkley, R. Cote, F. Chu. "Molecular architecture of photoreceptor phosphodiesterase." J Mol Biol, epub ahead of print, 2014

325. J. Erzberger, F. Stengel, R. Pellarin, S. Zhang, T. Schaefer, C. Aylett, P. Cimermancic, D. Boehringer, A. Sali, R. Aebersold, N. Ban. "Molecular architecture of the 40Sâ�¢eIF1â�¢eIF3 translation initiation complex." Cell 158, 1125-1135, 2014.

326. D. Schneidman-Duhovny, R. Pellarin, A. Sali. "Uncertainty in Integrative Structural Modeling." Curr Opin Struct Biol, 96-104, 2014.

327. P. Cimermancic, M.H. Medema, J. Claesen, K. Kurita, L. Wieland Brown, K. Mavrommatis, A. Pati, P.A. Godfrey, M. Koehrsen, J. Clardy, B.W. Birren, E. Takano, A. Sali, R.G. Linington, M. Fischbach. "Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters." Cell 158, 412-421, 2014.

328. M.H. Medema, P. Cimermancic, A. Sali, E. Takano, M. Fischbach. "A systematic computational analysis of biosynthetic gene cluster evolution: Lessons for engineering biosynthesis." submitted.

329. S.J. Kim, J. Fernandez-Martinez, P. Sampathkumar, A. Martel, T. Matsui, H. Tsuruta, T. Weiss, A. Markina-Inarrairaegui, J. Bonanno, M. Sauder, S. Burley, S. Almo, M. Rout, A. Sali. "Integrative Structure-Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex." Mol Cell Proteomics, epub ahead of print, 2014.

330. Y. Shi, J. Fernandez-Martinez, E. Tjioe, R. Pellarin, S.J. Kim, R. Williams, D. Schneidman, A. Sali, M. Rout, B. Chait. "Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex." MolCellProteomics, epub ahead of print, 2014.

331. B. Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. In: Current Protoc Bioinformatics, 47, pp. 5.6.1-5.6.32, John Wiley and Sons, 2014.


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332. E. Verschueren, J. Von Dollen, P. Cimermancic, N. Gulbahce, A. Sali, N. Krogan. Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Curr Protoc Bioinformatics 49, 8.19.1-8.19.16, 2015. PMCID4378866

333. A. Politis, C. Schmidt, E. Tjioe, A. Sandercock, K. Lasker, Y. Gordiyenko, D. Russel, A. Sali, C. Robinson. Topological models of heteromeric protein assemblies from mass spectrometry: Application to the yeast eIF3:eIF5 complex. Chem Biol 22, 117-128, 2015. PMCID4306531

334. J. Kollman, C. Greenberg, S. Li, M. Moritz, A. Zelter, K. Fong, J. Fernandez, A. Sali, J. Kilmartin, T. Davis, D. Agard. Ring closure activates yeast γTuRC for species-specific microtubule nucleation. Nat Struct Mol Biol 22, 132-137, 2015. PMCID4318760

335. J. Johnson, S. Santos, U. Pieper, A. Sali, N. Krogan, P. Beltrao. Prediction of functionally important phospho-regulatory events in Xenopus laevis oocytes. PLOS Comp Bio 11, e1004362, 2015. PMCID4552029

336. A. Sali, H. Berman, T. Schwede, J. Trewhella, G. Kleywegt, S. Burley, J. Markley, H. Nakamura, P. Adams, A. Bonvin, W. Chiu, M. Dal Peraro, F. Di Maio, T. Ferrin, K. Grunewald, A. Gutmanas, R. Henderson, G. Hummer, K. Iwasaki, G. Johnson, C. Lawson, J. Meiler, M. Marti-Renom, G. Montelione, M. Nilges, R. Nussinov, A. Patwardhan, J. Rappsilber, R. Read, H. Saibil, G. Schroder, C. Schwieters, C. Seidel, D. Svergun, M. Topf, E. Ulrich, S. Velanker, J. Westbrook. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 23, 1156-67, 2015. PMCID4933300

337. L. Carter, S.J. Kim, D. Schneidman-Duhovny, J. Stoehr, G. Poncet-Montange, T. Weiss, H. Tsuruta, S. Prusiner, A. Sali. Prion protein-antibody complexes characterized by chromatography-coupled small-angle X-ray scattering. Biophys J 109, 793-805, 2015. PMCID4547163

338. Y. Shi, R. Pellarin, P. Fridy, J. Fernandez-Martinez, M. Thompson, Y. Li, Q.J. Wang, A. Sali, M. Rout, B. Chait. "A strategy for dissecting the architectures of native macromolecular assemblies." Nat Methods 12, 1135-8, 2015.

339. J. Luo, P. Cimermancic, S. Viswanath, C. Ebmeier, B. Kim, M. Dehecq, V. Raman, C. Greenberg, R. Pellarin, A. Sali, D. Taatjes, S. Hahn, J. Ranish. Architecture of the human and yeast general transcription and DNA repair factor TFIIH. Mol Cell 59, 794-806, 2015. PMCID4560838

340. P. Robinson, M. Trnka, R. Pellarin, C. Greenberg, D. Bushnell, R. Davis, A. Burlingame, A. Sali, R. Kornberg. Molecular architecture of the yeast Mediator complex. eLife 4, e08719, 2015. PMCID4631838

341. R. Reid, M. Sgobba, B. Raveh, G. Rastelli, A. Sali, D. Santi. Analytical and simulation-based models for drug release and gel-degradation in a Tetra-PEG hydrogel drug-delivery system. Macromolecules 48, 7359-7369, 2015

342. C. Smith, K. Lin, A. Stecula, A. Sali, N. Shah. FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors. Leukemia 29, 2390-2, 2015. PMCID4675689

343. A.R. Choudhury, E. Sikorska, J. van den Boom, P. Bayer, L. Popenda, K. Szutkowski, S. Jurga, M. Bonomi, A. Sali, I. Zhukov, S. Passamonti, M. Novič. Structural model of the Bilitranslocase transmembrane domain supported by NMR and FRET data. PloS One 10, e0135455, 2015. PMCID4546402


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344. T. Rettenmaier, H. Fan, J. Karpiak, A. Doak, A. Sali, B. Shoichet, J. Wells. Small-molecule allosteric modulators of the protein kinase PDK1 from structure-based docking. J Med Chem 58, 8285-91, 2015

345. J. LoPiccolo, S.J. Kim, Y. Shi, B. Wu, H. Wu, B.T. Chait, R.H. Singer, A. Sali, M. Brenowitz, A.R. Bresnick, J.M. Backer. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer. J Biol Chem 290, 30390-405, 2015.

346. Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J. Mol. Biol. 428, 709-19, 2016. PMCID4794384

347. E. Lasater, E. Massi, A. Stecula, J. Politi, S. Tan, C. Smith, M. Gunthorpe, J. Holmes, F. Chehab, A. Sali, N. Shah. Novel TKI-resistant BCR-ABL1 Gatekeeper Residue Mutations Retain in vitro Sensitivity to Axitinib. Leukemia 30, 1405-9, 2016.

348. D. Schneidman-Duhovny, N. Khuri, G.Q. Dong, M. Winter, E. Shifrut, N. Friedman, C. Craik, P. Paz, F. Aswad, A. Sali. Predicting T-cell epitopes by integrated modeling of APC processing, MHCII presentation, and TCR recognition. Submitted

349. Sprowl J, Ong SS, Gibson A, Hu S, Du G, Lin W, Li L, Bharill S, Ness R, Stecula A, Offer S, Diasio R, Nies A, Schwab M, Cavaletti G, Schlatter E, Ciarimboli G, Schellens J, Isacoff E, Sali A, Chen T, Baker S, Sparreboom A, Pabla N. A phosphotyrosine switch regulates organic cation transporters. Nat Commun 7, 10880, 2016. PMCID4799362

350. M.F. Lensink, S. Velankar, A. Kryshtafovych, S. Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N. Fernandez-Fuentes, S. Viswanath, R. Elber, S. Grudinin, P. Popov, E. Neveu, H. Lee, M. Baek, S. Park, L. Heo, G.R. Lee, C. Seok, S. Qin, H. Zhou, D.W. Ritchie, B. Maigret, M. Devignes, A. Ghoorah, M. Torchala, R.A.G. Chaleil, P.A. Bates, E. Ben-Zeev, M. Eisenstein, S.S. Negi, Z. Weng, T. Vreven, B.G. Pierce, T.M. Borrman, J. Yu, F. Ochsenbein, R. Guerois, A. Vangone, J.P.G.L.M. Rodrigues, G. van Zundert, M. Nellen, L. Xue, E. Karaca, A.S.J. Melquiond, K. Visscher, P.L. Kastritis, A.M.J.J. Bonvin, X. Xu, L. Qiu, C. Yan, J. Li, Z. Ma, J. Cheng, X. Zou, Y. Shen, L.X. Peterson, H. Kim, A. Roy, X. Han, J. Esquivel-Rodriguez, D. Kihara, X. Yu, N.J. Bruce, J.C. Fuller, R.C. Wade, I. Anishchenko, P.J. Kundrotas, I.A. Vakser, K. Imai, K. Yamada, T. Oda, T. Nakamura, K. Tomii, C. Pallara, M. Romero-Durana, B. Jiménez-García, I.H. Moal, J. Férnandez-Recio, J.Y. Joung, J.Y. Kim, K. Joo, J. Lee, D. Kozakov, S. Vajda, S. Mottarella, D.R. Hall, D. Beglov, A. Mamonov, B. Xia, T. Bohnuud, C.A. Del Carpio, E. Ichiishi, N. Marze, D. Kuroda, S.S.R. Burman, J.J. Gray, E. Chermak, L. Cavallo, R. Oliva, A. Tovchigrechko, S.J. Wodak. Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment. Proteins, Epub ahead of print. PMCID5030136

351. B. Raveh, J.M. Karp, S. Sparks, K. Dutta, M.P. Rout, A. Sali, D. Cowburn. Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. Proc Natl Acad Sci USA 113, E2489-97, 2016. PMCID4983827

352. D. Schneidman, M. Hammel, J. Tainer, A. Sali. FoXS, FoXSDock, and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res 44, W424-9, 2016. PMCID4987932

353. Z.A. Chen, R. Pellarin, L. Fischer, A. Sali, M. Nilges, P.N. Barlow, J. Rappsilber. Structure of complement C3(H2O) revealed by quantitative cross-linking/mass spectrometry and modelling. Mol Cell Proteomics 15, 2730-2743, 2016. PMCID4974347


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354. B. Webb, A. Sali. Comparative Protein Structure Modeling Using MODELLER. In: Curr Protoc Protein Sci, 86, pp. 2.9.1-2.9.37, John Wiley and Sons, 2016.

355. J.C. Watts, K. Giles, D.J. Saltzberg, B.N. Dugger, S. Patel, A. Oehler, S. Bhardwaj, A. Sali, S.B. Prusiner. Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions. J Virol, in press.

356. U. Schulze-Gahmen, I. Echeverria, G. Stjepanovic, Y. Bai, H. Lu, D. Schneidman-Duhovny, J.A. Doudna, Q. Zhou, A. Sali, J.H. Hurley. Insights into HIV-1 proviral transcription from the structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. eLife 5, e15910, 2016.

357. Timney BL, Raveh B, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, Rout MP. Simple rules for passive diffusion through the nuclear pore complex. J Cell Biol. 2016 Oct 10;215(1):57-76. PMID: 27697925

358. Barkan DT, Cheng X, Celino H, Tran T, Bhandari A, Craik CS, Sali A, Smythe ML. Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. BMC Bioinformatics 17, 481, 2016. PMCID5120537

359. Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A. A Residue Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions. J Phys Chem B, in press.

360. Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell, in press.

361. C.H. Greenberg, J. Kollman, A. Zelter, R. Johnson, M.J. MacCoss, T.N. Davis, D.A. Agard, A. Sali. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. J Struct Biol 194, 303-10, 2016. PMCID4866596

362. B. Webb, A. Sali. "Comparative Protein Structure Modeling Using MODELLER." In: Curr Protoc Bioinformatics, 54, pp. 5.6.1-5.6.37, John Wiley and Sons, 2016.

363. P. Fromme, A. Sali. "Editorial overview: Biophysical and molecular biological methods." Curr Opin Struct Biol 40, ix-xi, 2016.

364. A. Jahangiri, S.W. Han, M.K. Sidorov, W. Chen, J. Rick, D. Schneidman-Duhovny, S. Mascharak, M. De Lay, J.R. Wagner, B. Imber, P.M. Flanigan, A. Chandra, R. Kuang, B.A. Castro, K. Lu, G. Bergers, A. Sali, W.A. Weiss, M.K. Aghi. Cross-activating c-Met/β1 integrin complex drives metastasis and invasive resistance in cancer. Proc Natl Acad Sci USA 114, E8685-E8694, 2017. PMCID5642678

365. X. Wang, P. Cimermancic, C. Yu, A. Schweitzer, N. Chopra, J.L. Engel, C. Greenberg, A.S. Huszagh, F. Beck, E. Sakata, Y. Yang, E.J. Novitsky, A. Leitner, P. Nanni, A. Kahraman, X. Guo, J.E. Dixon, S.D. Rychnovsky, R. Aebersold, W. Baumeister, A. Sali, L. Huang. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Mol Cell Proteomics 16, 840-854, 2017. PMCID5417825

366. N. Khuri, A. Zur, M. Wittwer, L. Lin, S.W. Yee, A. Sali, K. Giacomini. Computational Discovery And Experimental Validation of Inhibitors of the Human Intestinal Transporter, OATP2B1. J Chem Inf Model 57, 1402-1413, 2017.


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367. A. Chen, M. Vieth, D. Timm, C. Humblet, D. Schneidman-Duhovny, I.E. Chemmama, A. Sali, J. Lu, L. Liu. Reconstruction of 3D structures of MET Antibodies from Electron Microscopy 2D Class Averages. PloS One 12, e0175758, 2017. PMCID5391116

368. E.C. Chen, N. Khuri, X. Liang, A. Stecula, H. Chien, S.W. Yee, Y. Huang, A. Sali, K.M. Giacomini. Discovery of competitive and non-competitive ligands of the organic cation transporter 1 (OCT1; SLC22A1). J Med Chem 60, 2685-2696, 2017.

369. B. Webb, A. Sali. Protein structure modeling with MODELLER. In: Meth Mol Biol, 1654, pp. 39-54, 2017.

370. P. Upla, S.J. Kim, P. Sampathkumar, K. Dutta, S.M. Cahill, I.E. Chemmama, R. Williams, J.B. Bonanno, W.J. Rice, D.L. Stokes, D. Cowburn, S.C. Almo, A. Sali, M.P. Rout, J. Fernandez-Martinez. "Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex." Structure, 2017.

371. P.T. Manna, S. Obado, C. Boehm, C. Gadelha, G. van Miero, A. Sali, B. Chait, M. Rout, M.C. Field. "Lineage-specific proteins essential for endocytosis in trypanosomes." J Cell Sci 130, 1379-1392, 2017.

372. A. Stecula, A. Schlessinger, K. Giacomini, A. Sali. Human concentrative nucleoside transporter 3 (hCNT3, SLC28A3) forms a cyclic homotrimer. Biochemistry 56, 3475-3483, 2017

373. C.Y. Zhou, C.I. Stoddard, J.B. Johnston, M.J. Trnka, I. Echeverria, E. Palovcak, A. Sali, A.L. Burlingame, Y. Cheng, G.J. Narlikar. "Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones." Cell Rep 19, 2033-2044, 2017.

374. S.K. Burley, G. Kurisu, J.L. Markley, H. Nakamura, S. Velankar, H.M. Berman, A. Sali, T. Schwede, J. Trewhella. "PDB-Dev: A Prototype System for Depositing Integrative/Hybrid Structural Models." Structure. 2017 Sep 5;25(9):1317-1318. doi: 10.1016/j.str.2017.08.001. PubMed PMID: 28877501; PubMed Central PMCID:/> PMC5821105.

375. J. Trewhella, A.P Duff, D. Durand, F. Gabel, J.M. Guss, W.A. Hendrickson, G.L. Hura, D.A. Jacques, N.M. Kriby, A.H. Kwan, J. Perez, L. Pollack, T.M. Ryan, A. Sali, D. Schneidman-Duhovny, T. Schwede, D.I. Svergun, M. Sugiyama, J.A. Tainer, P. Vachette, J. Westbrook, A.E. Whitten. "2017 Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update." Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):710-728. doi:/> 10.1107/S2059798317011597. Epub 2017 Aug 18. PubMed PMID: 28876235; PubMed/> Central PMCID: PMC5586245.

376. S. Viswanath, M. Bonomi, S.J. Kim, V.A. Klenchin, K.C. Taylor, K.C. Yabut, N.T. Umbreit, H.A. Van Epps, J. Meehl, M.H. Jones, D. Russel, J.A. Velazquez-Muriel, M. Winey, I. Rayment, T.N. Davis, A. Sali, E.G. Muller. "The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling." Mol Biol Cell. 2017 Nov 7;28(23):3298-3314. doi: 10.1091/mbc.E17-06-0397. Epub 2017 Aug 16. PubMed PMID: 28814505; PubMed Central PMCID: PMC5687031.

377. S. Viswanath, I. Chemmama, P. Cimermancic, A. Sali. "Validating Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures." submitted.


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378. M.B. Winter, F. La Greca, S. Arastu-Kapur, P. Cimermancic, T.J. Buchholz, F. Caiazza, J.L. Anderl, M. Ravalin, M.F. Bohn, A. Sali, A.J. O’Donoghue, C.S. Craik. Immunoproteasome Functions Explained by Divergence in Cleavage Specificity and Regulation. eLife 6, e27364, 2017. PMCID5705213

379. X. Wang, I.E. Chemmama, C. Yu, A. Huszagh, Y. Xu, R. Viner, S.A. Block, P. Cimermancic, S. Rychnovsky, Y. Ye, A. Sali, L. Huang. The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress. J Biol Chem 292, 16310-16320, 2017. PMCID5625060

380. B. Webb, S. Viswanath, M. Bonomi, R. Pellarin, C.H. Greenberg, D. Saltzberg, A. Sali. Integrative structure modeling with the Integrative Modeling Platform. Prot Sci 27, 245-258, 2018. PMCID5734277

381. T. Yoshizawa, R. Ali, H.Y.J. Fung, K.A. Burke, Y. Lin, S.J. Kim, J. Jiou, M. Soniat, R. Oldenbourg, A. Sali, N.L. Fawzi, M.K. Rosen, Y.M. Chook. Nuclear import receptor inhibits phase separation of FUS through binding to multiple sites. Cell 173, 693-705, 2018.

382. S. Calhoun, M. Korczynska, D.J. Wichelecki, B. San Francisco, S. Zhao, D.A. Rodionov, M.W. Vetting, N.F. Al-Obaidi, H. Lin, M.J. O’Meara, D.A. Scott, J.H. Morris, D. Russel, S.C. Almo, A.L. Osterman, J.A. Gerlt, M.P. Jacobson, B.K. Shoichet, A. Sali. Prediction of enzymatic pathways by integrative pathway mapping. eLife 7, e31097, 2018. PMCID5788505

383. A.J. Guy, V. Irani, J.G. Beeson, B. Webb, A. Sali, J.S. Richards, P.A. Ramsland. Proteome-wide mapping of immune features onto Plasmodium protein three-dimensional structures. Sci Rep 8, 4355, 2018. PMCID5847524

384. S.J. Kim, J. Fernandez-Martinez, I. Nudelman, Y. Shi, W. Zhang, B. Raveh, T. Herricks, B.D. Slaughter, J. Hogan, P. Upla, I.E. Chemmama, R. Pellarin, I. Echeverria, M. Shivaraju, A.S. Chaudhury, J. Wang, R. Williams, J.R. Unruh, C.H. Greenberg, E.Y. Jacobs, Z. Yu, M.J. de la Cruz, R. Mironska, D.L. Stokes, J.D. Aitchison, M.F. Jarrold, J.L. Gerton, S.J. Ludtke, C.W. Akey, B.T. Chait, A. Sali, M.P. Rout. Integrative Structure and Functional Anatomy of a Nuclear Pore Complex. Nature 555, 475-482, 2018.

385. B. Vallat, B. Webb, J. Westbrook, A. Sali, H.M. Berman. Development of a prototype system for archiving integrative/hybrid structure models of biological macromolecules. Structure, S0969-2126(18)30092-3 [Epub ahead of print], 2018.

386. J. Singla, K.M. McClary, K.L. White, F. Alber, A. Sali, R.C. Stevens. Opportunities and challenges in building a spatiotemporal multi-scale model of the human pancreatic β-cell. Cell 173, 11-19, 2018.

387. A. Lyon, A. Zelter, S. Viswanath, A. Maxwell, R. Johnson, K.C.B. Yabut, M. MacCoss, T.N. Davis, E. Muller, A. Sali, D.A. Agard. Spc110 N-Terminal Domains Act Independently to Mediate Stable γ-Tubulin Small Complex Binding and γ-Tubulin Ring Complex Assembly. submitted.


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SIGNIFICANT PUBLICATIONS 1. Comparative protein modelling by satisfaction of spatial restraints

A Sali, TL Blundell Journal of Molecular Biology 234, 779-815, 1993

Dr. Sali conceived and performed the research, as well as wrote the paper.

2. How does a protein fold? A Sali, E. Shakhnovich, M Karplus Nature 369, 248-251, 1994

Dr. Sali conceived of the research, performed it, and co-wrote the paper.

3. Determining the architectures of macromolecular assemblies F Alber, S Dokudovskaya, LM Veenhoff, W Zhang, J Kipper, D Devos, ... Nature 450 (7170), 683-694, 2007

Dr. Sali conceived of the research, performed part of it, and co-wrote the paper.

4. Integrative Structure and Functional Anatomy of a Nuclear Pore Complex 4. S.J. Kim, J. Fernandez-Martinez, I. Nudelman, Y. Shi, W. Zhang, B. Raveh, T. Herricks, B.D. Slaughter, J. Hogan, P. Upla, I.E. Chemmama, R. Pellarin, I. Echeverria, M. Shivaraju, A.S. Chaudhury, J. Wang, R. Williams, J.R. Unruh, C.H. Greenberg, E.Y. Jacobs, Z. Yu, M.J. de la Cruz, R. Mironska, D.L. Stokes, J.D. Aitchison, M.F. Jarrold, J.L. Gerton, S.J. Ludtke, C.W. Akey, B.T. Chait, A. Sali, M.P. Rout Nature 555, 475-482, 2018

Dr. Sali co-led the research and co-wrote the paper.

5. Prediction of enzymatic pathways by integrative pathway mapping S. Calhoun, M. Korczynska, D.J. Wichelecki, B. San Francisco, S. Zhao, D.A. Rodionov, M.W. Vetting, N.F. Al-Obaidi, H. Lin, M.J. O’Meara, D.A. Scott, J.H. Morris, D. Russel, S.C. Almo, A.L. Osterman, J.A. Gerlt, M.P. Jacobson, B.K. Shoichet, A. Sali eLife 7, e31097, 2018

Dr. Sali conceived of the research and co-wrote the paper.

ACADEMIC LEADERSHIP Dr. Sali is involved in the leadership of Protein Data Bank, the key community database in structural biology. His roles have included membership on the Scientific Advisory Board, organizing a number of PDB workshops, and contributing as well as leading the writing of White Papers that made recommendations about the organization of the PDB and validation of various types of structures deposited in the database. In particular, Dr. Sali has co-led the establishment of PDB-Dev, the nascent PDB archive for integrative structures.

OTHER CREATIVE ACTIVITIES OTHER MENTORING: 2004-now Coaching of iPQB student journal club presentations (approx. 3 students each year). 2006-now The Academic Advisor for approximately one third of students in BMI.


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2008-now Coaching iPQB graduate students on submitting NSF research proposals.

Dates Name Program Role 2004 Nima Fayazmanesh Biophysics Supervised Graduate Rotation 2003 Greg Friedland Biophysics Supervised Graduate Rotation 2005 Michael Mysinger PSPG Supervised Graduate Rotation 2004 Dale Webster BMI Supervised Graduate Rotation 2003 Alex Adai BMI Supervised Graduate Rotation 2003 Brian Tuch BMI Supervised Graduate Rotation 2006 Alan Barber PSPG Supervised Graduate Rotation 2008 Adam Marko BMI Supervised Graduate Rotation 2008 Rocco Varela BMI Supervised Graduate Rotation 2004 Tiba Ayunechi BMI Thesis Committee member 2004 Barbara Novak BMI Orals Committee member 2004 Alan Graves Biophysics Orals Committee member 2004-now Alexandra Schnoes BMI Orals, thesis Committee member 2005 Ben Sellers Biophysics Orals Committee member 2005 Nathan Salomonis PSPG Orals Committee member 2005 Jerome Nilmeir Biophysics Orals Committee member 2005-07 Tuan Pham BMI Orals, Thesis Committee member 2006-07 Marco Sorani BMI Thesis committee member 2006-07 David Lomelin BMI Orals Committee member 2006-08 Ben Sellers BMI Thesis committee member 2006 Nima Fayazmanesh Biophysics Orals Committee member 2006 Arjun Narayanan Biophysics Orals Committee member 2006 Veena Thomas PSPG Orals Committee member 2006 Dale Webster BMI Orals Committee member 2006 Holly Atkinson BMI Orals Committee member 2006 Dan Mandel BMI Orals Committee member 2006-now Mike Keiser BMI Orals, Thesis Committee Member 2007-now Elisabeth Humphris Biophysics Orals, Thesis Committee member 2007-now Colin A. Smith BMI Orals Committee member 2005-08 Greg Friedland Biophysics Orals, Thesis Committee member 2007 Rafaela Ferreira BMI Orals Committee member 2007 Michelle Dimon BMI Orals Committee member 2007 Michael Hicks PSPG Orals Committee member 2008 Matt Eames Biophysics Thesis Committee member


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2008 Jason Fernandez PSPG Orals Committee member 2008 Leonard Apeltsin BMI Orals, Thesis Committee member 2009 Alan Barber PSPG Orals Committee member 2009 Hannes Braberg Biophysics Orals Committee member 2009 Noah Ollikainen BMI Orals, Thesis Committee member 2009 Peter Skewes-Cox BMI Orals Committee member 2009 Monica Tremont Biophysics Orals Committee member 2009 Kiyoshi Egami Biophysics Orals Committee member 2009 Martin Turk Visiting Scholar 2010 Rocco Varela BMI Thesis Committee member 2010 Russell Spitzer BMI Orals Committee member 2010 Henry Lin BMI Orals Committee member 2010 Jeremy Phillips BMI Thesis Committee member 2010 Geoff Rollins Biophysics Orals Committee member 2010 Laurens Kraal BMI Orals Committee member 2010 Ethan Geier PSPG Orals Committee member 2010 Davide Bau Visiting Scholar 2010 Benjamin Schwartz Visiting Scholar 2010 Yannick Spill Visting Scholar 2011 Brittany Fotsch CCB Supervised Graduate Rotation 2011 Zac Apte Biophysics Orals Committee member 2011 Yi Song BMI Supervised Graduate Rotation 2011 Argyris Politis Visiting Scholar 2011 Amrita Choudhury Visiting Scholar 2011 Javona White Bear BMI Supervised Graduate Rotation 2011 Natalia Khuri Biophysics Supervised Graduate Rotation 2011 Pia Unverdorben Visiting Scholar 2011 Bart Lenselink Visiting Scholar 2011 Yannick Spill Visiting Scholar 2012 Sara Calhoun Biophysics Supervised Graduate Rotation 2012 Diego Garrido Ruiz Biophysics Supervised Graduate Rotation 2012 Kale Kundert Biophysics Supervised Graduate Rotation 2012 Adrian Stecula PSPG Supervised Graduate Rotation 2012 Miriam Sgobba Visiting Scholar 2012 Jeff Yunes Bioengineering Orals Committee member 2012 James Webber BMI Orals Committee member 2013 Kyle Barlow iPQB Orals Committee member


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2013 Joel Karpiak CCB Orals Committee member 2013 Rahel Woldeyes CCB Orals Committee member 2013 Andrew Vanbenschoten Biophysics Thesis Committee member 2013 Daniel Himmelstein BMI Orals Committee member 2014 Dorota Latek Visiting Scholar 2014 Ilan Chemmama Biophysics Supervised Graduate Rotation 2014 Melissa Lemke Visiting Scholar 2014 Reed Stein PSPG Supervised Summer Rotation 2014 Leo Gendelev Biophysics Orals Committee member 2014 Ibai Irastorza Visiting Scholar 2015 Yiran Wu Visiting Scholar 2015 Seth Axen Bioinformatics Supervised Graduate Rotation 2015 Leon Bichman Visiting Scholar 2015 Sam Ivry PSPG Quals Committee Member 2015 Rebecca Davidson BMI Quals Committee Member 2015 Neville Bethel Biophysics Quals Committee Member 2015 Sara Calhoun Biophysics Thesis Committee Member

2015 Diego Garrido Ruiz Biophysics Thesis Committee Member

2015 Kale Kundert Biophysics Thesis Committee Member

2016 Daniel Himmelstein Bioinformatics Thesis Committee Member

2016 Ilan Chemmama Biophysics Thesis Committee Member

2016 Charles Greenberg Biophysics Thesis Committee Member

2016 Bruk Mensa CCB Quals Committee Member 2016 James Webber BMI Quals Committee Member 2016 Elena Caceres BMI Quals Committee Member 2016 Kyle Barlow BMI Thesis Committee Member

2017 Kale Kundert Biophysics Thesis Committee Member

2017 Charlotte Nelson BMI Thesis Committee Member

2017 Alexander Wolff Biophysics Thesis Committee Member


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2017 Benjamin Barad Biophysics Thesis Committee Member

2018 James Lucas Bioengineering Thesis Committee Member

ORGANIZATION OF MEETINGS: 1999-2001

Program Committee, Georgia Tech Intl. Conference on Bioinformatics, Atlanta GA

2001 Program Committee, Math/Chem/Comp 2001, Dubrovnik, Croatia 2005 Program Committee, Protein Society 19th Symposium in Boston, MA 2005 Program Committee, Protein Structure Modeling Workshop, Rutgers University,NJ 2006 Program Committee, American Society for Biochemistry and Molecular Biology 2007 Program Committee, 4th Conference on Modeling of Protein Interactions (MPI) 2008 Organizer, Workshop on Applications of Protein Structure Models in Biomedical

Research, UCSF, CA 2010 Program Committee, 3DSIG symposium at ISMB conference, Boston 2010 Co-Organizer, Keystone Symposia on Frontiers in Structural Biology 2012 Co-Organizer, Keystone Symposia on High-Throughput Structural Biology 2012 Co-Organizer, Conference on Structural Analysis of Supramolecular Assemblies by

Hybrid Methods, Lake Tahoe 2013 Organizer, Keystone Symposia on Structural Analysis of Supramolecular Assemblies

by Hybrid Methods, Lake Tahoe 2014 Organizer, Martin Karplus Celebration Symposium 2006-now 2019

Organizer, World Molecular Engineering Network, annual TSRI & UCSF meeting in San Jose del Cabo, Mexico Organizer, 63rd Annual Meeting of the Biophysical Society, Baltimore, MD, Mar 2-6, 2019.

FELLOWSHIPS TO LAB MEMBERS: Howard Hughes Predoctoral Fellowship (R. Sanchez) Howard Hughes Predoctoral Fellowship (F. Davis) Burroughs Wellcome Fund Predoctoral Fellowship (R. Chiang) Alfred P. Sloan Postdoctoral Fellowship (A. Stuart) Burroughs Wellcome Fund Postdoctoral Fellowship (A. Fiser, M.A. Marti-Renom) Rockefeller University Presidential Fellowship (M.A. Marti-Renom) Charles Revson Foundation Postdoctoral Fellowship (A. Fiser, M.S. Madhusudhan) NIH Postdoctoral Fellowship (R. Karchin) Burroughs Wellcome Predoctoral Fellowship (M. Kim, R. Chiang) DOE Predoctoral Fellowship (M. Peterson) Genentech Award (M. Peterson) Human Frontier Sciences Program Postdoctoral Fellowship (F. Foerster) Spanish Minister of Education Postdoctoral Fellowship (J. Velazquez) Clore Foundation Predoctoral Fellowship (K. Lasker)


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Weizmann Institute Advancing Women in Science Postdoctoral Fellowship (D. Schneidman) UC Cancer Research Coordinating Committee Fellowship (D. Barkan) NIH NRSA Postdoctoral Fellowship (A. Schlessinger) Chancellor’s Graduate Research Fellowship (P. Cimermancic) Swiss National Science Foundation Perspective Researcher Fellowship (R. Pellarin) NSC Taiwan Postdoctoral Fellowship (B. Chen) NSF Graduate Research Fellowship (C. Greenberg) Howard Hughes Medical Institutes Predoctoral Fellowship (P. Cimermancic) Frank M. Goyan Award for Excellence in Physical Chemistry (J. Phillips) 2012 School of Pharmacy Research Award (P. Cimermancic) QB3 Rogers Award (P. Cimermancic) NIH Fellowship (K. Stafford) PhRMA Fellowship in Pharmacology/Toxicology (A. Stecula) Mel Jones Excellence in Graduate Student Research Award (C. Greenberg) PhRMA Fellowship in Pharmacology/Toxicology (A. Stecula) AFPE Pre-Doctoral Award in Pharmaceutical Science (A. Stecula) NSF Fellowship (I. Chemmama) SOFTWARE: 1993 MODELLER, a program for comparative protein structure modeling by satisfaction of spatial restraints; licensed to Accelrys Inc. since 1994. 2000 MODPIPE, a program for large-scale comparative protein structure modeling; licensed to Accelrys Inc. and Structural Genomix Pharmaceuticals Inc. (2000-2004). 2000 MODBASE, a comprehensive database of comparative protein structure models; licensed to Structural Genomix Pharmaceuticals Inc. (2000-2004). 2010 IMP, a program for integrative structure determination of macromolecular assemblies, open source.

Documents

20180606 AndrejSali CurriculumVitae...2018/06/06 · 2016 Speaker at the EMBL Distinguished Lecture Series, Heidelberg, Germany, January 12, 2016. 2016 Organizer and Speaker at the